EP3262190B1 - Biomarker panel for the detection of cancer - Google Patents

Biomarker panel for the detection of cancer Download PDF

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EP3262190B1
EP3262190B1 EP16710678.0A EP16710678A EP3262190B1 EP 3262190 B1 EP3262190 B1 EP 3262190B1 EP 16710678 A EP16710678 A EP 16710678A EP 3262190 B1 EP3262190 B1 EP 3262190B1
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mir
methylation
cancer
sample
marker
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EP3262190A1 (en
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Barbara BURWINKEL
Rongxi YANG
Andreas Schneeweiss
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Universitaet Heidelberg
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the present invention relates to a method, a kit and a device for diagnosing breast cancer.
  • the method comprises determining panels of methylation and miRNA markers.
  • Cancer is one of the most important medical and health problems in the world. As the leading cause of death worldwide, there were 12.4 million new cancer cases and 7.6 million cancer related deaths in 2008. It has been predicted that the deaths from cancer worldwide is continuously rising and 12 million deaths would be caused by cancer in the year of 2030.
  • Breast cancer is the most common cancer among women. About one out of nine women will develop breast cancer during her life ( Feuer, E.J., et al., The lifetime risk of developing breast cancer. J Natl Cancer Inst 85, 892-897 (1993 )). Worldwide approximately 1.3 million women develop breast cancer each year. Mortality rates have continued to decrease over the years due to all the efforts and advances made in early diagnosis and treatment ( Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D.
  • ovarian cancer Compared to BC, ovarian cancer (OvCa) is comparable rare in occurrence, but is the leading cause of death from gynecologic cancers because of its high malignancy. In 2008, 225,000 women were diagnosed with ovarian cancer worldwide, and 140,000 of these women died from the disease. Typically, women with the OvCa present with few early symptoms, and thus nearly three-quarters of ovarian cancer cases present at an advanced stage, with the disease spread well beyond the ovaries. Pancreatic cancer (PaCa) is the most aggressive of all epithelial malignancies. With 279,000 new diagnoses of PaCa worldwide, the 5-year overall survival rate of PaCa patients is less than 5%. Although recent genome-wide association studies (GWAS) have successfully detected several genetic variants associated with the risk of BC, OvCa and PaCa, no valuable marker for the early detection of BC has been identified.
  • GWAS genome-wide association studies
  • MBC Metastatic breast cancer
  • Circulating tumor cells have been proposed as an FDA approved independent prognostic marker for metastasis, specifically for progression-free survival and overall survival.
  • a cardinal cut off of greater than 5 CTCs per 7.5ml of blood has been defined as CTC positive ( Cristofanilli M, Budd GT, Ellis MJ, Stopeck A, et al; Circulating tumor cells, disease progression, and survival in metastatic breast cancer; N Engl J Med. 2004 Aug 19;351(8):781-91 ).
  • CTC positive Cristofanilli M, Budd GT, Ellis MJ, Stopeck A, et al; Circulating tumor cells, disease progression, and survival in metastatic breast cancer; N Engl J Med. 2004 Aug 19;351(8):781-91 .
  • Beside CTCs also protein based circulating tumor markers like carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA 15-3) are widely used as prognostic markers, as well as in monitoring breast cancer treatment success and follow-up ( Uehara M, Kinoshita T, Hojo T, Akashi-Tanaka S, Iwamoto E, Fukutomi T. Long-term prognostic study of carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA 15-3) in breast cancer.
  • CEA carcinoembryonic antigen
  • CA 15-3 carbohydrate antigen 15-3
  • Epigenetic changes are defined as changes in gene expression that are not due to any alterations in the genomic DNA sequence. Aberrant epigenetic signatures have been considered as a hallmark of human cancer ( Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8, 286-298 (2007 ).).
  • DNA methylation has critical roles in the control of gene activities and in the architecture of the nucleus of the cell Weber, M., et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37, 853-862 (2005 )). Furthermore, unlike genetic markers or variants, DNA methylation is principally reversible.
  • DNA methylation profile of specific genes are considered as therapeutic targets ( Mack, G.S. Epigenetic cancer therapy makes headway. J Natl Cancer Inst 98, 1443-1444 (2006 )).
  • DNA methylation may serve as a link between environmental factors and the genome. DNA methylation modulated by environmental factors or aging may alter the expression of critical genes of cells and consequently induce malignant transformation of cells or even a cancer ( Widschwendter, M., et al. Epigenotyping in peripheral blood cell DNA and breast cancer risk: a proof of principle study. P LoS One 3, e2656 (2008 )).
  • MiRNAs are small, non-coding RNAs ( ⁇ 18-25 nucleotides in length) that regulate gene expression on a post-transcriptional level by degrading mRNA molecules or blocking their translation ( Bartel DP.: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-97 ). Hence, they play an essential role in the regulation of a large number of biological processes, including cancer ( Calin GA, Chester CD, Shimizu M, Bichi R, Zupo S, Rick E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, et al.
  • Circulating miRNAs are defined as miRNAs present in the cell-free component of body fluids like plasma, serum, and the like. Lawrie et al. ( Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, Banham AH, Pezzella F, Boultwood J, Wainscoat JS, Hatton CS, Harris AL. Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol 2008; 141:672-5 ) were among the first to demonstrate the presence of miRNAs in bodily fluids.
  • WO 2013/190091 A1 identifies miR-801, miR-148b, miR-376c, miR-376a, miR-652, miR-409 and miR-127 as breast cancer markers.
  • the amount of the individual markers is measured. Measuring the entire group of microRNA markers in combination with the methylation status of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4 is not disclosed, nor is any synergistic effect of measuring the miRNAs in combination with at least one of the methylation markers, which can be measured in healthy subjects and in BC patients.
  • the present invention relates to a method of diagnosing breast cancer (BC) in a subject, comprising (a) determining the methylation status of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4, and (b) determining the amount of the miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and miR-148b in a subject, wherein the methylation status of the at least one methylation marker and the presence of the miRNAs is indicative of the risk of said subject to suffer from BC.
  • the present invention relates to the use of a kit for diagnosing BC, comprising
  • the present invention relates to a device for identifying BC, comprising: (a) an analyzing unit comprising (i) a detection agent for determining the methylation status of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P and DYRK4, and (ii) a detection agent for determining the presence of: miR-652, miR-801, miR-376c, miR-376a, miR-376a, miR-127, miR-409 and miR-148b in a sample of a subject; and (b) an evaluation unit comprising a data processor having tangibly embedded an algorithm for carrying out a comparison of the amount determined by the analyzing unit with a reference and which is capable of generating an output file containing a diagnosis established based on the said comparison.
  • an analyzing unit comprising (i) a detection agent for determining the methylation status of at least one methylation marker selected from
  • Nucleic acid molecules are understood as a polymeric or oligomeric macromolecule made from nucleotide monomers. Nucleotide monomers are composed of a nucleobase, a five-carbon sugar (such as but not limited to ribose or 2'-deoxyribose), and one to three phosphate groups. Typically, a polynucleotide is formed through phosphodiester bonds between the individual nucleotide monomers. In the context of the present invention referred to nucleic acid molecules include but are not limited to ribonucleic acid (RNA), deoxyribonucleic acid (DNA), and mixtures thereof such as e.g. RNA-DNA hybrids.
  • RNA ribonucleic acid
  • DNA deoxyribonucleic acid
  • mixtures thereof such as e.g. RNA-DNA hybrids.
  • nucleic acids can e.g. be synthesized chemically, e.g. in accordance with the phosphotriester method (see, for example, Uhlmann, E. & Peyman, A. (1990) Chemical Reviews, 90, 543-584 ).
  • Aptamers are nucleic acids which bind with high affinity to a polypeptide, here mir146-a. Aptamers can be isolated by selection methods such as SELEmir146-a (see e.g. Jayasena (1999) Clin. Chem., 45, 1628-50 ; Klug and Famulok (1994) M. Mol.
  • RNA molecules from a large pool of different single-stranded RNA molecules.
  • Aptamers can also be synthesized and selected in their mirror-image form, for example as the L-ribonucleotide ( Nolte et al. (1996) Nat. Biotechnol., 14, 1116-9 ; Klussmann et al. (1996) Nat. Biotechnol., 14, 1112-5 ).
  • L-ribonucleotide Nolte et al. (1996) Nat. Biotechnol., 14, 1116-9 ; Klussmann et al. (1996) Nat. Biotechnol., 14, 1112-5 .
  • Nucleic acids may be degraded by endonucleases or exonucleases, in particular by DNases and RNases which can be found in the cell. It is, therefore, advantageous to modify the nucleic acids in order to stabilize them against degradation, thereby ensuring that a high concentration of the nucleic acid is maintained in the cell over a long period of time ( Beigelman et al. (1995) Nucleic Acids Res. 23:3989-94 ; WO95/11910 ; WO98/37240 ; WO97/29116 ). Typically, such a stabilization can be obtained by introducing one or more internucleotide phosphorus groups or by introducing one or more non-phosphorus internucleotides.
  • Suitable modified internucleotides are compiled in Uhlmann and Peyman (1990), supra (see also Beigelman et al. (1995) Nucleic Acids Res. 23:3989-94 ; WO95/11910 ; WO98/37240 ; WO 97/29116 ).
  • Modified internucleotide phosphate radicals and/or non-phosphorus bridges in a nucleic acid which can be employed in one of the uses according to the invention contain, for example, methyl phosphonate, phosphorothioate, phosphoramidate, phosphorodithioate and/or phosphate esters, whereas non-phosphorus internucleotide analogues contain, for example, siloxane bridges, carbonate bridges, carboxymethyl esters, acetamidate bridges and/or thioether bridges. It is also the intention that this modification should improve the durability of a pharmaceutical composition which can be employed in one of the uses according to the invention.
  • Nucleic acids may be selected from the group consisting of, a peptide nucleic acid (PNA), a locked nucleic acid (LNA), a glycol nucleic acid (GNA), a threose nucleic acid (TNA), a microRNA (miRNA), and a small interfering RNA (siRNA), a polynucleotide probe, a primer(s) (e.g. a primer pair), in particular a primer(s) for polymerase chain reaction (PCR), reverse transcription (RT) reaction, or DNA sequencing.
  • PNA peptide nucleic acid
  • LNA locked nucleic acid
  • GNA glycol nucleic acid
  • TAA threose nucleic acid
  • miRNA microRNA
  • siRNA small interfering RNA
  • a polynucleotide probe e.g. a primer pair
  • PCR polymerase chain reaction
  • RT reverse transcription
  • nucleic acid comprises genomic DNA, cDNA, recombinant DNA, cRNA, mRNA, microRNA (miRNA) and small interfering RNA (siRNA).
  • a nucleic acid may consist of an entire gene, or a portion thereof.
  • the nucleic acid can also be an artificial nucleic acid.
  • Artificial nucleic acids include polyamide or peptide nucleic acid (PNA), morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is distinguished from naturally-occurring DNA or RNA by changes to the backbone of the molecule as well known to the person skilled in the art.
  • miRNA short ribonucleic acid
  • miRNA include human miRNAs, mature single stranded miRNAs, precursor miRNAs (pre-miR), and variants thereof, which may be naturally occurring.
  • miRNA also includes primary miRNA transcripts (pri-miRNAs) and duplex miRNAs. Unless otherwise noted, when used herein, the name of a specific miRNA refers to the mature miRNA.
  • MiRNA-precursor may consists of 25 to several thousand nucleotides, typically 40 to 130, 50 to 120, or 60 to 110 nucleotides. Typically, a mature miRNA consists of 5 to 100 nucleotides, often 10 to 50, 12 to 40, or 18 to 26 nucleotides.
  • miRNA also includes the "guide" strand which eventually enters the RNA-induced silencing complex (RISC) as well as to the "passenger” strand complementary thereto.
  • RISC RNA-induced silencing complex
  • miRNAs The sequence of several miRNAs is known in the art and readily assessable to the skilled person via well-known sequence databases, such as e.g. miRBase (http://www.mirbase.org/), ( Griffiths-Jones S., NAR 2004 32(Database Issue):D109-D111 ; Kozomara A, Griffiths-Jones S., NAR 2011 39(Database Issue):D152-D157 ).
  • miRBase http://www.mirbase.org/
  • database accession numbers of the individual miRNAs are those of miRNAs of human origin.
  • these database entries also provide the database accession numbers of the respective miRNA of different origin, such as e.g. mirNAs of any mammal, reptile, or bird origin, such
  • miR-652 is deposited at miRBase ID MI0003667 which comprises hsa-miR-652-3p (MIMAT0003322) and hsa-miR-652-5p (MIMAT0022709), which corresponds to SEQ ID NO: 1 and 2, respectively, of the present invention.
  • miR-801 was deposited at miRBase ID MI0005202: 5'-GAUUGCUCUGCGUGCGGAAUCGAC-3', however, it is now considered as a fragment of U11 spliceosomal RNA and was thus remove from miRBase.
  • the pre-miRNA-801 is located at chr1: 28847698 - 28847793. Its sequence corresponds to SEQ ID NO: 3 of the present invention.
  • miR-376c also referred to as miR-368, is deposited at miRBase ID MI0000776, which comprises miR-376c-3p (MIMAT0000720) and hsa-miR-376c-5p (MIMAT0022861), which corresponds to SEQ ID NO: 4 and 5, respectively, of the present invention.
  • miR-376a is deposited at miRBase ID MI0000784, which comprises hsa-miR-376a-3p (MIMAT0000729) and hsa-miR-376a-5p (MIMAT0003386), which corresponds to SEQ ID NO: 6 and 7, respectively, of the present invention.
  • miR-127 is deposited at miRBase ID MI0000472, which comprises hsa-miR-127-3p (MIMAT0000446) and hsa-miR-127-5p (MIMAT0004604), which corresponds to SEQ ID NO: 8 and 9, respectively, of the present invention.
  • miR-409 is deposited at miRBase ID MI0001735, which comprises hsa-miR-409-3p (MIMAT0001639) and hsa-miR-409-5p (MIMAT0001638), which corresponds to SEQ ID NO: 10 and 11, respectively, of the present invention.
  • miR-148b The sequence of miR-148b is deposited at miRBase ID MI0000811, which comprises hsa-miR-148b-3p (MIMAT0000759) and hsa-miR-148b-5p (MIMAT0004699), which corresponds to SEQ ID NO: 12 and 13, respectively, of the present invention.
  • the term "combination of miRNAs” relates to combinations of the miRNAs of the present invention.
  • the amount of a miRNA can be determined in a sample of a subject by techniques well known in the art. Depending on the nature of the sample, the amount may be determined by PCR based techniques for quantifying the amount of a polynucleotide or by other methods like mass spectrometry or (next generation) sequencing or one of the methods described in the examples ( Cissell KA, Deo SK. Trends in microRNA detection. Anal Bioanal Chem. 2009;394(4):1109-1116 or de Planell-Saguer M, Rodicio MC. Analytical aspects of microRNA in diagnostics: a review.
  • determining the amounts of at least the miRNAs of a combination of miRNAs preferably relates to determining the amount of each of the miRNAs of the combination separately in order to be able to compare the amount of each miRNA of the combination to a reference specific for said miRNA.
  • probe refers to a single-strand oligonucleotide which is typically used for the detection of target RNA and/or DNA sequences that is complementary to the sequence of the probe.
  • a probe hybridizes to single-stranded nucleic acid (DNA or RNA) whose nucleotide sequence allows for nucleotide pairing due to complementarity between the probe and the target sequence.
  • the length of a probe depends on the intended use as well as the required specificity of the probe. Typically, a probe is 20-500 (i.e.
  • probes are used in various experimental set ups such as but not limited to Southern and Northern Blots, for real-time PCR and In Situ Hybridization (ISH) as well as for microarray experiments.
  • a probe may be unlabeled, directly labelled, or indirectly labelled, such as with biotin to which a streptavidin complex may later bind.
  • Said label may be a molecule detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means.
  • suitable labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and other entities which are or can be made detectable.
  • a label may be incorporated into nucleic acids at any position, e.g. at the 3' end, at the 5' end or internally.
  • probe also encompasses nucleic acids differing in the composition of their backbone such as but not limited to peptide nucleic acids (PNAs), locked nucleic acids (LNAs), glycol nucleic acids (GNAs) and threose nucleic acids (TNAs).
  • PNAs peptide nucleic acids
  • LNAs locked nucleic acids
  • GNAs glycol nucleic acids
  • TAAs threose nucleic acids
  • primer refers to a single-strand oligonucleotide which typically serves as a starting point for DNA-replicating enzymes.
  • a primer binds to or hybridises with a DNA template and typically comprises a sequence being complementary to the DNA sequence to which it is supposed to bind.
  • a primer may also comprise additional sequences e.g. sequences serving as nuclease cleavage sites (e.g. Bam HI, Hind III, etc.).
  • the length of a primer is chosen depending on the intended use. For instance, primers used for the amplification of DNA in Polymerase-Chain Reactions (PCR) typically have a length of at least 10 nucleotides, preferably between 10 to 50 (i.e.
  • primers are used for sequencing of DNA templates.
  • primer also encompassed in the term "primer” are "degenerate primers" which are a mixture of similar, but not identical primers.
  • a primer may be tagged or labelled with a marker molecule detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means.
  • the term "expression level" refers to the amount of gene product present in the body or a sample at a certain point of time.
  • the expression level can e.g. be measured/quantified/detected by means of the protein or mRNA expressed from the gene.
  • the expression level can for example be quantified by normalizing the amount of gene product of interest present in a sample with the total amount of gene product of the same category (total protein or mRNA) in the same sample or a reference sample (e.g. a sample taken at the same time from the same individual or a part of identical size (weight, volume) of the same sample) or by identifying the amount of gene product of interest per defined sample size (weight, volume, etc.).
  • the expression level can be measured or detected by means of any method as known in the art, e.g. methods for the direct detection and quantification of the gene product of interest (such as mass spectrometry) or methods for the indirect detection and measurement of the gene product of interest that usually work via binding of the gene product of interest with one or more different molecules or detection means (e.g. primer(s), probes, antibodies, protein scaffolds) specific for the gene product of interest.
  • detection means e.g. primer(s), probes, antibodies, protein scaffolds
  • the determination of the level of gene copies comprising also the determination of the absence or presence of one or more fragments (e.g. via nucleic acid probes or primers, e.g. quantitative PCR, Multiplex ligation-dependent probe amplification (MLPA) PCR) is also within the knowledge of the skilled artisan.
  • MLPA Multiplex ligation-dependent probe amplification
  • Proteins usable in the present invention can be further modified by chemical modification.
  • chemical modification comprises other chemical groups than the 20 naturally occurring amino acids. Examples of such other chemical groups include without limitation glycosylated amino acids and phosphorylated amino acids.
  • Chemical modifications of a polypeptide may provide advantageous properties as compared to the parent polypeptide, e.g. one or more of enhanced stability, increased biological half-life, or increased water solubility.
  • Chemical modifications applicable to the variants usable in the present invention include without limitation: PEGylation, glycosylation of non-glycosylated parent polypeptides, or the modification of the glycosylation pattern present in the parent polypeptide.
  • peptide refers to a short polymer of amino acids linked by peptide bonds. It has the same chemical (peptide) bonds as proteins, but is commonly shorter in length.
  • the shortest peptide is a dipeptide, consisting of two amino acids joined by a single peptide bond. There can also be a tripeptide, tetrapeptide, pentapeptide, etc.
  • the peptide has a length of up to 8, 10, 12, 15, 18 or 20 amino acids.
  • a peptide has an amino end and a carboxyl end, unless it is a cyclic peptide.
  • polypeptide refers to a single linear chain of amino acids bonded together by peptide bonds and preferably comprises at least about 21 amino acids.
  • a polypeptide can be one chain of a protein that is composed of more than one chain or it can be the protein itself if the protein is composed of one chain.
  • the term "protein” refers to a molecule comprising one or more polypeptides that resume a secondary and tertiary structure and additionally refers to a protein that is made up of several polypeptides, i.e. several subunits, forming quaternary structures.
  • the protein has sometimes non-peptide groups attached, which can be called prosthetic groups or cofactors.
  • the primary structure of a protein or polypeptide is the sequence of amino acids in the polypeptide chain.
  • the secondary structure in a protein is the general three-dimensional form of local segments of the protein. It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
  • the secondary structure is defined by patterns of hydrogen bonds between backbone amide and carboxyl groups.
  • the tertiary structure of a protein is the three-dimensional structure of the protein determined by the atomic coordinates.
  • the quaternary structure is the arrangement of multiple folded or coiled protein or polypeptide molecules molecules in a multi-subunit complex.
  • post-translational used herein refers to events that occur after the translation of a nucleotide triplet into an amino acid and the formation of a peptide bond to the proceeding amino acid in the sequence.
  • post-translational events may occur after the entire polypeptide was formed or already during the translation process on those parts of the polypeptide that have already been translated.
  • Post-translational events typically alter or modify the chemical or structural properties of the resultant polypeptide.
  • post-translational events include but are not limited to events such as glycosylation or phosphorylation of amino acids, or cleavage of the peptide chain, e.g. by an endopeptidase.
  • co-translational used herein refers to events that occur during the translation process of a nucleotide triplet into an amino acid chain. Those events typically alter or modify the chemical or structural properties of the resultant amino acid chain.
  • co-translational events include but are not limited to events that may stop the translation process entirely or interrupted the peptide bond formation resulting in two discreet translation products.
  • segment refers to any part of a macromolecule (e.g. a polypeptide, protein or polyprotein) into which this macromolecule can be divided.
  • a macromolecule may consist of one or more segments. Such segmentation may exist due to functional (e.g. having immunoreactive features or membrane attachment functions) or structural (e.g. nucleotide or amino acid sequence, or secondary or tertiary structure) properties of the macromolecule and/or the individual segment.
  • functional e.g. having immunoreactive features or membrane attachment functions
  • structural e.g. nucleotide or amino acid sequence, or secondary or tertiary structure
  • an “epitope”, also known as antigenic determinant, is the segment of a macromolecule that is recognized by the immune system, specifically by antibodies, B cells, or T cells. Such epitope is that part or segment of a macromolecule capable of binding to an antibody or antigen-binding fragment thereof.
  • binding preferably relates to a specific binding.
  • epitopes usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three-dimensional structural characteristics, as well as specific charge characteristics. Conformational and non-conformational epitopes are distinguished in that the binding to the former but not the latter is lost in the presence of denaturing solvents.
  • domain refers to the segment of a protein or polyprotein sequence or structure (or corresponding nucleotide sequence) that can evolve, function, and/or exist independently of the rest of the protein chain.
  • a protein consists of one or several domains with each of them being three-dimensional structure that are stable and folded independently of the rest of the protein chain.
  • Such domain typically forms an independent functional unit within the protein (e.g. transmembrane-domains, immunoglobulin-like domains, or DNA-binding domains).
  • amino acid sequence of several peptides and proteins, as well as the nucleotide sequences encoding the respective peptides and proteins are well known in the art and readily assessable to the skilled person via well-known sequence databases, such as e.g. Genbank (http://www.ncbi.nlm.nih.gov/genbank/). It is understood that below indicated database accession numbers of the individual sequence are those of human origin. However these database entries also provide the database accession numbers of the respective nucleotide sequences of different origin, such as e.g. amino acid or nucleotides sequences of any mammal, reptile, or bird origin, such as e.g. those selected from the group consisting of laboratory animals (e.g.
  • mice or rat can be domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, and gorillas nucleotide amino acid or nucleotides sequences.
  • domestic animals including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard
  • primates including chimpanzees, bonobos, and gorillas nucleotide amino acid or nucleotides sequences.
  • variant is to be understood as a polynucleotide or protein which differs in comparison to the polynucleotide or protein from which it is derived by one or more changes in its length or sequence.
  • the polypeptide or polynucleotide from which a protein or nucleic acid variant is derived is also known as the parent polypeptide or polynucleotide.
  • variant comprises "fragments” or “derivatives” of the parent molecule. Typically, “fragments” are smaller in length or size than the parent molecule, whilst “derivatives” exhibit one or more differences in their sequence in comparison to the parent molecule.
  • modified molecules such as but not limited to post-translationally modified proteins (e.g. glycosylated, biotinylated, phosphorylated, ubiquitinated, palmitoylated, or proteolytically cleaved proteins) and modified nucleic acids such as methylated DNA.
  • modified molecules such as but not limited to post-translationally modified proteins (e.g. glycosylated, biotinylated, phosphorylated, ubiquitinated, palmitoylated, or proteolytically cleaved proteins) and modified nucleic acids such as methylated DNA.
  • variants such as but not limited to RNA-DNA hybrids.
  • a variant is constructed artificially, preferably by gene-technological means whilst the parent polypeptide or polynucleotide is a wild-type protein or polynucleotide.
  • variants are to be understood to be encompassed by the term "variant" as used herein.
  • variants usable in the present invention may also be derived from homologs, orthologs, or paralogs of the parent molecule or from artificially constructed variant, provided that the variant exhibits at least one biological activity of the parent molecule, i.e. is functionally active.
  • a variant usable in the present invention exhibits a total number of up to 200 (up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200) changes in the amino acid or nucleotide sequence (i.e. exchanges, insertions, deletions, 5'-, 3'-, N-terminal, and/or C-terminal truncations). Amino acid exchanges may be conservative and/or non-conservative.
  • a variant usable in the present invention differs from the protein or polynucleotide from which it is derived by up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acid or nucleic acid exchanges.
  • a "variant" as used herein can be characterized by a certain degree of sequence identity to the parent polypeptide or parent polynucleotide from which it is derived. More precisely, a protein variant in the context of the present invention exhibits at least 80% sequence identity to its parent polypeptide.
  • a polynucleotide variant in the context of the present invention exhibits at least 80% sequence identity to its parent polynucleotide.
  • the sequence identity of protein variants is over a continuous stretch of 20, 30, 40, 45, 50, 60, 70, 80, 90, 100 or more amino acids.
  • the sequence identity of polynucleotide variants is over a continuous stretch of 60, 90, 120, 135, 150, 180, 210, 240, 270, 300 or more nucleotides.
  • sequence identity is used throughout the specification with regard to polypeptide and polynucleotide sequence comparisons. This expression preferably refers to a sequence identity of at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to the respective reference polypeptide or to the respective reference polynucleotide.
  • the polypeptide in question and the reference polypeptide exhibit the indicated sequence identity over a continuous stretch of 20, 30, 40, 45, 50, 60, 70, 80, 90, 100 or more amino acids or over the entire length of the reference polypeptide.
  • the polynucleotide in question and the reference polynucleotide exhibit the indicated sequence identity over a continuous stretch of 60, 90, 120, 135, 150, 180, 210, 240, 270, 300 or more nucleotides or over the entire length of the reference polypeptide.
  • a fragment may be naturally occurring (e.g. splice variants) or it may be constructed artificially, preferably by gene-technological means.
  • a fragment (or deletion variant) has a deletion of up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acids or nucleic acids as compared to the parent polypeptide.
  • the sequence identity is to be calculated with reference to the longer of the two sequences to be compared, if not specifically indicated otherwise. If the reference sequence is indicated, the sequence identity is determined on the basis of the full length of the reference sequence indicated by SEQ ID, if not specifically indicated otherwise.
  • sequence alignments can be carried out with several art-known algorithms, preferably with the mathematical algorithm of Karlin and Altschul ( Karlin & Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5877 ), with hmmalign (HMMER package, http://hmmer.wustl.edu/) or with the CLUSTAL algorithm ( Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-80 ) available e.g.
  • sequence identity may be calculated using e.g.
  • BLAST, BLAT or BlastZ or BlastX.
  • BLASTN and BLASTP programs Altschul et al. (1990) J. Mol. Biol. 215: 403-410 .
  • Hybridization can also be used as a measure of sequence identity or homology between two nucleic acid sequences.
  • a nucleic acid sequence encoding F, N, or M2-1, or a portion of any of these can be used as a hybridization probe according to standard hybridization techniques.
  • the hybridization of an F, N, or M2-1 probe to DNA or RNA from a test source is an indication of the presence of the F DNA or RNA, N DNA or RNA, or M2-1 DNA or RNA, respectively, in the test source.
  • Hybridization conditions are known to those skilled in the art and can be found, for example, in Current Protocols in Molecular Biology, John Wiley & Sons, N. Y., 6.3.1-6.3.6, 1991 .
  • Mode hybridization conditions are defined as equivalent to hybridization in 2X sodium chloride/sodium citrate (SSC) at 30°C, followed by a wash in 1X SSC, 0.1% SDS at 50°C.
  • Highly stringent conditions are defined as equivalent to hybridization in 6X sodium chloride/sodium citrate (SSC) at 45°C, followed by a wash in 0.2 X SSC, 0.1 % SDS at 65°C.
  • Typical substitutions are among the aliphatic amino acids, among the amino acids having aliphatic hydroxyl side chain, among the amino acids having acidic residues, among the amide derivatives, among the amino acids with basic residues, or the amino acids having aromatic residues.
  • Typical semi-conservative and conservative substitutions are: Amino acid Conservative substitution Semi-conservative substitution A G; S; T N; V; C C A; V; L M; I; F; G D E; N; Q A; S; T; K; R; H E D; Q; N A; S; T; K; R; H F W; Y; L; M; H I; V; A G A S; N; T; D; E; N; Q H Y; F; K; R L; M; A I V; L; M; A F; Y; W; G K R; H D; E; N; Q; S; T; A L M; I; V; A F; Y; W; H; C M L; I; V; A F; Y; W; C; N Q D; E; S; T; A; G; K; R P V; I L; A; M; W; Y; S; T; C; F Q N D; E; A; S; T; L; M; K; R
  • tissue refers to an ensemble of cells of the same origin which fulfil a specific function concertedly.
  • tissue include but are not limited to connective tissue, muscle tissue, nervous tissue, and epithelial tissue. Multiple tissues together form an "organ” to carry out a specific function.
  • organ include but are not limited to glands, muscle, blood, brain, heart, liver, kidney, stomach, skeleton, joint, and skin.
  • disease and “disorder” are used interchangeably herein, referring to an abnormal condition, especially an abnormal medical condition such as an illness or injury, wherein a tissue, an organ or an individual is not able to efficiently fulfil its function anymore.
  • a disease is associated with specific symptoms or signs indicating the presence of such disease. The presence of such symptoms or signs may thus, be indicative for a tissue, an organ or an individual suffering from a disease. An alteration of these symptoms or signs may be indicative for the progression of such a disease.
  • a progression of a disease is typically characterised by an increase or decrease of such symptoms or signs which may indicate a "worsening" or “bettering” of the disease.
  • the "worsening" of a disease is characterised by a decreasing ability of a tissue, organ or organism to fulfil its function efficiently, whereas the “bettering" of a disease is typically characterised by an increase in the ability of a tissue, an organ or an individual to fulfil its function efficiently.
  • a tissue, an organ or an individual being at "risk of developing" a disease is in a healthy state but shows potential of a disease emerging.
  • the risk of developing a disease is associated with early or weak signs or symptoms of such disease. In such case, the onset of the disease may still be prevented by treatment.
  • Examples of a disease include but are not limited to traumatic diseases, inflammatory diseases, infectious diseases, cutaneous conditions, endocrine diseases, intestinal diseases, neurological disorders, joint diseases, genetic disorders, autoimmune diseases, and various types of cancer.
  • Cancer refers to a proliferative disorder involving abnormal cell growth which may invade or spread to other tissues or organs of a subject. Cancers are classified by the type of cell that the tumor cells resemble and is therefore presumed to be the origin of the tumor. These types include but are not limited to carcinoma (cancers derived from epithelial cells) sarcoma (cancers arising from connective tissue such as e.g.
  • lymphoma and leukemia cancer arising from hematopoietic cells that leave the marrow and tend to mature in the lymph nodes and blood
  • germ cell tumor cancers derived from pluripotent cells
  • blastoma cancers derived from immature "precursor" cells or embryonic tissue.
  • cancer includes but is not limited to acute lymphoblastic leukemia (ALL), acute myeloid leukemia, adrenocortical carcinoma, AIDS-related cancers, AIDS-related lymphoma, anal cancer, appendix cancer, astrocytoma, childhood cerebellar or cerebral cancer, basal-cell carcinoma, bile duct cancer, extrahepatic, bladder cancer, bone tumor, osteosarcoma/malignant fibrous histiocytoma, brainstem glioma, brain cancer, brain tumor (cerebellar astrocytoma, cerebral astrocytoma/malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, visual pathway and hypothalamic glioma), breast cancer, bronchial adenomas/carcinoids, Burkitt's lymphoma, carcinoid tumor, central nervous system lymphoma, cerebellar a
  • breast tumor relates to an abnormal hyperproliferation of breast tissue cells in a subject, which may be a benign (non-cancerous) tumor or a malign (cancerous) tumor.
  • Benign breast tumors preferably, include fibroadenomas, granular cell tumors, intraductal papillomas, and phyllodes tumors.
  • a malign tumor is a breast cancer (BC) as specified herein above.
  • MBC metal breast cancer
  • ovary tumor relates to an abnormal hyperproliferation of ovary tissue cells in a subject, which may be a benign (non-cancerous) tumor or a malign (cancerous) tumor.
  • a malign tumor is an ovary cancer (OvaCa) as specified herein above.
  • pancreatic tumor relates to an abnormal hyperproliferation of ovary tissue cells in a subject, which may be a benign (non-cancerous) tumor or a malign (cancerous) tumor.
  • a malign tumor is a pancreatic cancer (PaCa) as specified herein above.
  • CTC circulating tumor cell
  • CTC status relates to the presence or absence of more than a reference amount of CTC in a sample.
  • the reference amount of CTC is 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, or 7.5 CTC / 7.5 ml blood, 5 CTC / 7.5 ml blood being more preferred.
  • the CTC status is unfavorable, indicating a low probability of successful treatment and a low progression-free and overall survival probability. Conversely, in subjects where a blood sample comprises less than said reference amount of CTC, the CTC status is favorable, indicating a high probability of successful treatment and a high progression-free and overall survival probability.
  • the amounts of the miRNAs used for determining the CTC status of a subject as defined herein below are indicative of the CTC status of a subject.
  • determining the CTC status in a subject as used herein relates to determining the amount or amounts of said miRNA or miRNAs and thus obtaining an indication of the subject's CTC status.
  • the status can be diagnosed to be "favorable” or "unfavorable”
  • Symptoms of a disease are implication of the disease noticeable by the tissue, organ or organism having such disease and include but are not limited to pain, weakness, tenderness, strain, stiffness, and spasm of the tissue, an organ or an individual.
  • “Signs” or “signals” of a disease include but are not limited to the change or alteration such as the presence, absence, increase or elevation, decrease or decline, of specific indicators such as biomarkers or molecular markers, or the development, presence, or worsening of symptoms.
  • indicator and “marker” are used interchangeably herein, and refer to a sign or signal for a condition or is used to monitor a condition.
  • a condition refers to the biological status of a cell, tissue or organ or to the health and/or disease status of an individual.
  • An indicator may be the presence or absence of a molecule, including but not limited to peptide, protein, and nucleic acid, or may be a change in the expression level or pattern of such molecule in a cell, or tissue, organ or individual.
  • An indicator may be a sign for the onset, development or presence of a disease in an individual or for the further progression of such disease.
  • An indicator may also be a sign for the risk of developing a disease in an individual.
  • the term "gene product” relates to a, preferably macromolecular, physical entity, the presence of which in a cell depends on the expression of said gene in said cell.
  • the mechanisms of gene expression are well-known to the one skilled in the art to include the basic mechanisms of transcription, i.e. formation of RNA corresponding to the said gene or parts thereof, and translation, i.e. production of polypeptide molecules having an amino acid sequence encoded by said RNA according to the genetic code; it is well-known to the one skilled in the art that other cellular processes may be involved in gene expression as well, e.g. RNA processing, RNA editing, proteolytic processing, protein editing, and the like.
  • gene product thus includes RNA, preferably mRNA, as well as polypeptides expressed from said gene. It is clear from the above that the term gene product also includes fragments of said RNA(s), preferably with a length of at least ten, at least twelve, at least 20, at least 50, or at least 100 nucleotides, and fragments (peptides) from said polypeptides, preferably with a length of at least eight, at least ten, at least twelve, at least 15, at least 20 amino acids.
  • Determining the amount of a gene product relates to measuring the amount of said gene product, preferably semi-quantitatively or quantitatively. Measuring can be done directly or indirectly. Preferably, measuring is performed on a processed sample, said processing comprising extraction of polynucleotides or polypeptides from the sample. It is, however, also envisaged by the present invention that the gene product is determined in situ, e.g. by immune-histochemistry (IHC)
  • the amount of the polynucleotides of the present invention can be determined with several methods well-known in the art.
  • Quantification preferably is absolute, i.e. relating to a specific number of polynucleotides or, more preferably, relative, i.e. measured in arbitrary normalized units.
  • a normalization is carried out by calculating the ratio of a number of specific polynucleotides and total number of polynucleotides or a reference amplification product.
  • Methods allowing for absolute or relative quantification are well known in the art.
  • quantitative PCR methods are methods for relative quantification; if a calibration curve is incorporated in such an assay, the relative quantification can be used to obtain an absolute quantification.
  • the polynucleotide amounts are normalized polynucleotide amounts, i.e. the polynucleotide amounts obtained are set into relation to at least one reference amplification product, thereby, preferably, setting the polynucleotide amounts into relation to the number of cells in the sample and/or the efficiency of polynucleotide amplification.
  • the reference amplification product is a product obtained from a polynucleotide known to have a constant abundancy in each cell, i.e. a polynucleotide comprised in most, preferably all, cells of a sample in approximately the same amount. More preferably, the reference amplification product is amplified from a chromosomal or mitochondrial gene or from the mRNA of a housekeeping gene.
  • the amout of polynucleotides could be determined by Shotgun sequencing, Bridge PCR, Sanger sequencing, pyrosequencing, next-generation sequecing, Single-molecule real-time sequencing, Ion Torrent sequencing, Sequencing by synthesis, Sequencing by ligation, Massively parallel signature sequencing, Polony sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, Single molecule real time (SMRT) sequencing, Nanopore DNA sequencing, Tunnelling currents DNA sequencing, Sequencing by hybridization, Sequencing with mass spectrometry, Microfluidic Sanger sequencing, Transmission electron microscopy DNA sequencing, RNA polymerase sequencing, In vitro virus high-throughput sequencing, Chromatin Isolation by RNA Purification (ChIRP-Seq), Global Run-on Sequencing (GRO-Seq), Ribosome Profiling Sequencing (Ribo-Seq)/ARTseq, RNA Immunoprecipitation Sequencing (RIP-Seq), High-Throughput Sequencing
  • the amount of peptides or polypeptides of the present invention can be determined in various ways.
  • Direct measuring relates to measuring the amount of the peptide or polypeptide based on a signal which is obtained from the peptide or polypeptide itself and the intensity of which directly correlates with the number of molecules of the peptide present in the sample.
  • a signal sometimes referred to as intensity signal -may be obtained, e.g., by measuring an intensity value of a specific physical or chemical property of the peptide or polypeptide.
  • Indirect measuring includes measuring of a signal obtained from a secondary component (i.e. a component not being the peptide or polypeptide itself) or a biological read out system, e.g., measurable cellular responses, ligands, labels, or enzymatic reaction products.
  • Determining the amount of a peptide or polypeptide can be achieved by all known means for determining the amount of a peptide in a sample.
  • Said means comprise immunoassay and / or immunohistochemistry devices and methods which may utilize labeled molecules in various sandwich, competition, or other assay formats.
  • Said assays will develop a signal which is indicative for the presence or absence of the peptide or polypeptide.
  • the signal strength can, preferably, be correlated directly or indirectly (e.g. reverse- proportional) to the amount of polypeptide present in a sample.
  • Further suitable methods comprise measuring a physical or chemical property specific for the peptide or polypeptide such as its precise molecular mass or NMR spectrum.
  • Said methods comprise, preferably, biosensors, optical devices coupled to immunoassays, biochips, analytical devices such as mass-spectrometers, NMR- analyzers, or chromatography devices. Further, methods include micro-plate ELISA-based methods, fully-automated or robotic immunoassays, Cobalt Binding Assays, and latex agglutination assays.
  • Determining the amount of a peptide or polypeptide comprises the step of measuring a specific intensity signal obtainable from the peptide or polypeptide in the sample.
  • a specific intensity signal may be the signal intensity observed at an m/z variable specific for the peptide or polypeptide observed in mass spectra or a NMR spectrum specific for the peptide or polypeptide.
  • Determining the amount of a peptide or polypeptide may, preferably, comprise the steps of (a) contacting the peptide with a specific ligand, (b) (optionally) removing non-bound ligand, (c) measuring the amount of bound ligand.
  • the bound ligand will generate an intensity signal.
  • Binding according to the present invention includes both covalent and non-covalent binding.
  • a ligand according to the present invention can be any compound, e.g., a peptide, polypeptide, nucleic acid, or small molecule, binding to the peptide or polypeptide described herein.
  • Preferred ligands include antibodies, nucleic acids, peptides or polypeptides such as receptors or binding partners for the peptide or polypeptide and fragments thereof comprising the binding domains for the peptides, and aptamers, e.g. nucleic acid or peptide aptamers.
  • Methods to prepare such ligands are well-known in the art. For example, identification and production of suitable antibodies or aptamers is also offered by commercial suppliers. The person skilled in the art is familiar with methods to develop derivatives of such ligands with higher affinity or specificity. For example, random mutations can be introduced into the nucleic acids, peptides or polypeptides.
  • antibody refers to secreted immunoglobulins which lack the transmembrane region and can thus, be released into the bloodstream and body cavities.
  • Antibodies are typically made of four polypeptide chains comprising two identical heavy chains and identical two light chains which are connected via disulfide bonds and resemble a "Y"-shaped macro-molecule. Papain digestion of antibodies produces two identical antigen binding fragments, called “Fab fragments” (also referred to as “Fab portion” or “Fab region”) each with a single antigen binding site, and a residual “Fc fragment” (also referred to as "Fc portion” or “Fc region”) whose name reflects its ability to crystallize readily.
  • the crystal structure of the human IgG Fc region has been determined ( Deisenhofer (1981) Biochemistry 20:2361-2370 ).
  • the Fc region is composed of two identical protein fragments, derived from the CH2 and CH3 domains of the antibody's two heavy chains; in IgM and IgE isotypes, the Fc regions contain three heavy chain constant domains (CH2 - 4) in each polypeptide chain.
  • CH2 - 4 heavy chain constant domains
  • Fab' fragment refers to a Fab fragment additionally comprising the hinge region of an Ig molecule whilst “F(a')2 fragments” are understood to comprise two Fab fragments being either chemically linked or connected via a disulfide bond.
  • sdAb single domain antibodies
  • scFv single chain Fv
  • Divalent single-chain variable fragments can be engineered by linking two scFvs (scFvA-scFvB). This can be done by producing a single peptide chain with two VH and two VL regions, yielding "tandem scFvs" (VHA-VLA-VHB-VLB).
  • Another possibility is the creation of scFvs with linkers that are too short for the two variable regions to fold together, forcing scFvs to dimerize. Usually linkers with a length of 5 residues are used to generate these dimers. This type is known as "diabodies”.
  • Bispecific diabodies are formed by expressing to chains with the arrangement VHA-VLB and VHB-VLA or VLA-VHB and VLB-VHA, respectively.
  • Single-chain diabodies (scDb) comprise a VHA-VLB and a VHB-VLA fragment which are linked by a linker peptide (P) of 12-20 amino acids, preferably 14 amino acids, (VHA-VLB-P-VHB-VLA).
  • Bi-specific T-cell engagers are fusion proteins consisting of two scFvs of different antibodies wherein one of the scFvs binds to T cells via the CD3 receptor, and the other to a tumor cell via a tumor specific molecule ( Kufer et al. (2004) Trends Biotechnol. 22:238-244 ).
  • Dual affinity retargeting molecules (“DART” molecules) are diabodies additionally stabilized through a C-terminal disulfide bridge.
  • the present invention also includes single chain antibodies and humanized hybrid antibodies wherein amino acid sequences of a non-human donor antibody exhibiting a desired antigen-specificity are combined with sequences of a human acceptor antibody.
  • the donor sequences will usually include at least the antigen-binding amino acid residues of the donor but may comprise other structurally and/or functionally relevant amino acid residues of the donor antibody as well.
  • Such hybrids can be prepared by several methods well known in the art.
  • the ligand or agent binds specifically to the peptide or polypeptide.
  • Specific binding according to the present invention means that the ligand or agent should not bind substantially to ("cross-react" with) another peptide, polypeptide or substance present in the sample to be analyzed.
  • the specifically bound peptide or polypeptide should be bound with at least 3 times higher, more preferably at least 10 times higher and even more preferably at least 50 times higher affinity than any other relevant peptide or polypeptide.
  • Nonspecific binding may be tolerable, if it can still be distinguished and measured unequivocally, e.g. according to its size on a Western Blot, or by its relatively higher abundance in the sample.
  • Binding of the ligand can be measured by any method known in the art. Preferably, said method is semi-quantitative or quantitative. Suitable methods are described in the following.
  • binding of a ligand may be measured directly, e.g. by NMR or surface plasmon resonance.
  • an enzymatic reaction product may be measured (e.g. the amount of a protease can be measured by measuring the amount of cleaved substrate, e.g. on a Western Blot).
  • the ligand may exhibit enzymatic properties itself and the "ligand/peptide or polypeptide" complex or the ligand which was bound by the peptide or polypeptide, respectively, may be contacted with a suitable substrate allowing detection by the generation of an intensity signal.
  • the amount of substrate is saturating.
  • the substrate may also be labeled with a detectable label prior to the reaction.
  • the sample is contacted with the substrate for an adequate period of time.
  • An adequate period of time refers to the time necessary for a detectable, preferably measurable, amount of product to be produced. Instead of measuring the amount of product, the time necessary for appearance of a given (e.g. detectable) amount of product can be measured.
  • the ligand may be coupled covalently or non-covalently to a label allowing detection and measurement of the ligand. Labelling may be done by direct or indirect methods. Direct labelling involves coupling of the label directly (covalently or non-covalently) to the ligand.
  • Indirect labelling involves binding (covalently or non-covalently) of a secondary ligand to the first ligand.
  • the secondary ligand should specifically bind to the first ligand.
  • Said secondary ligand may be coupled with a suitable label and/or be the target (receptor) of tertiary ligand binding to the secondary ligand.
  • the use of secondary, tertiary or even higher order ligands is often used to increase the signal intensity.
  • Suitable secondary and higher order ligands may include antibodies, secondary antibodies, and the well-known streptavidin-biotin system (Vector Laboratories, Inc.).
  • the ligand or substrate may also be "tagged" with one or more tags as known in the art.
  • tags may then be targets for higher order ligands.
  • Suitable tags include biotin, digoxygenin, His-Tag, Glutathion-S-Transferase, FLAG, GFP, myc-tag, influenza A virus haemagglutinin (HA), maltose binding protein, and the like.
  • the tag is preferably at the N-terminus and/or C-terminus.
  • Suitable labels are any labels detectable by an appropriate detection method. Typical labels include gold particles, latex beads, acridan ester, luminol, ruthenium, enzymatically active labels, radioactive labels, magnetic labels ("e.g.
  • Enzymatically active labels include e.g. horseradish peroxidase, alkaline phosphatase, beta-Galactosidase, Luciferase, and derivatives thereof.
  • Suitable substrates for detection include di-amino-benzidine (DAB), 3,3'-5,5'-tetramethylbenzidine, NBT-BCIP (4-nitro blue tetrazolium chloride and 5-bromo-4-chloro-3-indolyl-phosphate), CDP-StarTM (Amersham Biosciences), ECFTM (Amersham Biosciences).
  • a suitable enzyme-substrate combination may result in a colored reaction product, fluorescence or chemo luminescence, which can be measured according to methods known in the art (e.g. using a light-sensitive film or a suitable camera system).
  • fluorescent labels include fluorescent proteins (such as GFP and its derivatives), Cy3, Cy5, Texas Red, Fluorescein, and the Alexa dyes (e.g. Alexa 568). Further fluorescent labels are available e.g. from Molecular Probes (Oregon). Also the use of quantum dots as fluorescent labels is contemplated.
  • Typical radioactive labels include 35S, 1251, 32P, 33P and the like.
  • a radioactive label can be detected by any method known and appropriate, e.g. a light-sensitive film or a phosphor imager.
  • Suitable measurement methods according the present invention also include precipitation (particularly immunoprecipitation), electrochemiluminescence (electro-generated chemiluminescence), RIA (radioimmunoassay), ELISA (enzyme- linked immunosorbent assay), sandwich enzyme immune tests, electrochemiluminescence sandwich immunoassays (ECLIA), dissociation-enhanced lanthanide fluoro immuno assay (DELFIA), scintillation proximity assay (SPA), turbidimetry, nephelometry, latex-enhanced turbidimetry or nephelometry, or solid phase immune tests, like e.g.
  • reverse phase protein arrays or antibody arrays can be reverse phase protein arrays or antibody arrays.
  • Further methods known in the art such as gel electrophoresis, 2D gel electrophoresis, SDS polyacrylamid gel electrophoresis (SDS-PAGE), Western Blotting, and mass spectrometry, can be used alone or in combination with labelling or other detection methods as described above.
  • the amount of a peptide or polypeptide may also be determined as follows: (a) contacting a solid support comprising a ligand for the peptide or polypeptide as specified above with a sample comprising the peptide or polypeptide and (b) measuring the amount peptide or polypeptide which is bound to the support.
  • the ligand preferably chosen from the group consisting of nucleic acids, peptides, polypeptides, antibodies and aptamers, is preferably present on a solid support in immobilized form.
  • Materials for manufacturing solid supports include, inter alia, commercially available column materials, polystyrene beads, latex beads, magnetic beads, colloid metal particles, glass and/or silicon chips and surfaces, nitrocellulose strips, membranes, sheets, duracytes, wells and walls of reaction trays, plastic tubes etc.
  • the ligand or agent may be bound to many different carriers. Examples of well-known carriers include glass, polystyrene, polyvinyl chloride, polypropylene, polyethylene, polycarbonate, dextran, nylon, amyloses, natural and modified celluloses, polyacrylamides, agaroses, and magnetite.
  • the nature of the carrier can be either soluble or insoluble for the purposes of the invention.
  • Suitable methods for fixing/immobilizing said ligand are well known and include, but are not limited to ionic, hydrophobic, covalent interactions and the like. It is also contemplated to use "suspension arrays" as arrays according to the present invention ( Nolan 2002, Trends Biotechnol. 20(1):9-12 ).
  • the carrier e.g. a microbead or microsphere
  • the array consists of different microbeads or microspheres, possibly labeled, carrying different ligands.
  • Methods of producing such arrays for example based on solid-phase chemistry and photo-labile protective groups, are generally known ( US 5,744,305 ).
  • CpG site relates to a dinucleotide sequence 5'-CG-3' comprised in a polynucleotide, preferably comprised in DNA, more preferably comprised in genomic DNA of a subject.
  • the CpG sites to be analyzed according to the present invention are the CpG sites located in the intron, exon or promoter region of a gene of interest. In case the CpG sites are located in the promoter region, said region is preferably 3000 nucleotides, 2500 nucleotides, 2100 nucleotides, or 1750 nucleotides upstream of the translation start site of the respective gene of interest.
  • the CpG sites to be analyzed according to the present invention are the CpG sites located in the region 1750-3000 nucleotides, 2100-3000 nucleotides, or 2500-3000 nucleotides upstream of the translation start site of the gene of interest gene.
  • analysis of a CpG site corresponding to a CpG site of the present invention is also encompassed by the present invention.
  • the skilled person knows how to determine the CpG sites in a sample corresponding to the CpG sites detailed herein above, e.g. by determining the translation start site of the gene of interest and / or by aligning said sequence from a sample to the sequence of the gene of interest. Further, it is also envisaged by the present invention that the methylation status of other CpG sites is determined in addition to determining the methylation status of a CpG site of the present invention.
  • determining the methylation status relates to determining if a methyl group is present at the 5 position of the pyrimidine ring of a cytosine in a polynucleotide.
  • the cytosine residue is followed in 3' direction by a guanosine residue, the two residues forming a CpG site.
  • methylation-specific PCR MSP
  • BS-Seq whole genome bisulfite sequencing or other sequencing based methods
  • PBAT Post-Bisulfite Adapter Tagging
  • T-WGBS Tagmentation-Based Whole Genome Bisulfite Sequencing
  • Oxidative Bisulfite Sequencing oxBS-Seq
  • Tet-Assisted Bisulfite Sequencing TAB-Seq
  • Methylated DNA Immunoprecipitation Sequencing Methylation-Capture (MethylCap) Sequencing, Methyl-Binding-Domain - Capture (MBDCap) Sequencing, Reduced-Representation Bisulfite Sequencing (RRBS-Seq)
  • real-time PCR based methods of bisulfite treated DNA e.g.
  • Methylight restriction with a methylation-sensitive restriction enzyme, e.g. in the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)-Assay, pyrosequencing of bisulfite treated DNA, or the like AIMS, amplification of inter-methylated sites; BC-seq, bisulphite conversion followed by capture and sequencing; BiMP, bisulphite methylation profiling; BS, bisulphite sequencing; BSPP, bisulphite padlock probes; CHARM, comprehensive high-throughput arrays for relative methylation; COBRA, combined bisulphite restriction analysis; DMH, differential methylation hybridization; HELP, HpaII tiny fragment enrichment by ligation-mediated PCR; MCA, methylated CpG island amplification; MCAM, MCA with microarray hybridization; MeDIP, mDIP and mCIP, methylated DNA immunoprecipitation; MIRA, methylated CpG island recovery assay
  • the methylation status is determined by the methods described in the examples herein below, e.g. the sequencing-based Infinium 27K methylation assay or the mass spectrometry based method of MALDI-TOF mass spectrometry.
  • the methylation status of a specific cytosine residue in a specific polynucleotide molecule can only be "unmethylated” (meaning 0% methylation) or "methylated” (meaning 100% methylation).
  • the methylation status can be "unmethylated” (meaning 0% methylation, i.e. none of the two cytosine residues methylated), "hemimethylated” (meaning 50% methylation, i.e. one of the two cystosine residues methylated), or "methylated” or "fully methylated” (meaning 100% methylation, i.e.
  • an average methylation status is determined, which can e.g, preferably, be expressed as a percentage (% methylation), and which can assume any value between 0% and 100%. It is also understood by the skilled person, that the methylation status can be expressed as a percentage in case the average methylation of different cell populations is determined.
  • the blood cells according to the present invention are a mixture of variant cell types. It is possible that certain cell types have high methylation levels whereas other cell types have lower methylation levels, and finally reach an average methylation of e.g. 50 %.
  • the term "detection agent” relates to an agent specifically interacting with, and thus recognizing, the expression level of a gene of interest, the methylation status of a gene of interest, or the presence or amount of a miRNA of the present invention.
  • said detection agent is a protein, polypeptide, peptide, polynucleotide or an oligonucleotide.
  • the detection agent is labeled in a way allowing detection of said detection agent by appropriate measures. Labeling can be done by various techniques well known in the art and depending of the label to be used. Preferred labels to be used are fluorescent labels comprising, inter alia, fluorochromes such as fluorescein, rhodamin, or Texas Red.
  • the label may also be an enzyme or an antibody. It is envisaged that an enzyme to be used as a label will generate a detectable signal by reacting with a substrate. Suitable enzymes, substrates and techniques are well known in the art.
  • An detection agent to be used as label may specifically recognize a target molecule which can be detected directly (e.g., a target molecule which is itself fluorescent) or indirectly (e.g., a target molecule which generates a detectable signal, such as an enzyme).
  • the labeled detection agents of the sample will be contacted to the sample to allow specific interaction. Washing may be required to remove non-specifically bound detection agent which otherwise would yield false values. After this interaction step is complete, a researcher will place the detection device into a reader device or scanner.
  • a device for detecting fluorescent labels preferably, consists of some lasers, preferably a special microscope, and a camera.
  • the fluorescent labels will be excited by the laser, and the microscope and camera work together to create a digital image of the sample.
  • These data may be then stored in a computer, and a special program will be used, e.g., to subtract out background data.
  • the resulting data are, preferably, normalized, and may be converted into a numeric and common unit format.
  • the data will be analyzed to compare samples to references and to identify significant changes.
  • Comparing encompasses comparing the presence, absence or amount of an indicator referred to herein which is comprised by the sample to be analyzed with the presence, absence or amount of said indicator in a suitable reference sample. It is to be understood that comparing as used herein refers to a comparison of corresponding parameters or values, e.g., an absolute amount of the indicator as referred to herein is compared to an absolute reference amount of said indicator; a concentration of the indicator is compared to a reference concentration of said indicator; an intensity signal obtained from the indicator as referred to herein in a sample is compared to the same type of intensity signal of said indicator in a reference sample. The comparison referred to may be carried out manually or computer assisted.
  • the value of the determined amount may be compared to values corresponding to suitable references which are stored in a database by a computer program.
  • the computer program may further evaluate the result of the comparison by means of an expert system. Accordingly, the result of the identification referred to herein may be automatically provided in a suitable output format.
  • sample or “sample of interest” are used interchangeably herein, referring to a part or piece of a tissue, organ or individual, typically being smaller than such tissue, organ or individual, intended to represent the whole of the tissue, organ or individual.
  • a sample provides information about the tissue status or the health or diseased status of an organ or individual.
  • samples include but are not limited to fluid samples such as blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate, or tissue samples such as e.g. tissue extracts obtained from tumour tissue or tissue adjacent to a tumour.
  • tissue samples such as e.g. tissue extracts obtained from tumour tissue or tissue adjacent to a tumour.
  • cell cultures or tissue cultures such as but not limited to cultures of various cancer cells.
  • Samples can be obtained by well known techniques and include, preferably, scrapes, swabs or biopsies from the digestive tract, liver, pancreas, anal canal, the oral cavity, the upper aerodigestive tract and the epidermis. Such samples can be obtained by use of brushes, (cotton) swabs, spatula, rinse/wash fluids, punch biopsy devices, puncture of cavities with needles or surgical instrumentation. Tissue or organ samples may be obtained from any tissue or organ by, e.g., biopsy or other surgical procedures. More preferably, samples are samples of body fluids, e.g., preferably, blood, plasma, serum, urine, saliva, lacrimal fluid, and fluids obtainable from the breast glands, e.g. milk.
  • body fluids e.g., preferably, blood, plasma, serum, urine, saliva, lacrimal fluid, and fluids obtainable from the breast glands, e.g. milk.
  • the sample of a body fluid comprises cells of the subject.
  • Separated cells may be obtained from the body fluids or the tissues or organs by separating techniques such as filtration, centrifugation or cell sorting.
  • samples are obtained from those body fluids described herein below. More preferably, cells are isolated from said body fluids as described herein below.
  • Analysis of a sample may be accomplished on a visual or chemical basis.
  • Visual analysis includes but is not limited to microscopic imaging or radiographic scanning of a tissue, organ or individual allowing for morphological evaluation of a sample.
  • Chemical analysis includes but is not limited to the detection of the presence or absence of specific indicators or alterations in their amount or level.
  • reference sample refers to a sample which is analysed in a substantially identical manner as the sample of interest and whose information is compared to that of the sample of interest.
  • a reference sample thereby provides a standard allowing for the evaluation of the information obtained from the sample of interest.
  • a reference sample may be derived from a healthy or normal tissue, organ or individual, thereby providing a standard of a healthy status of a tissue, organ or individual. Differences between the status of the normal reference sample and the status of the sample of interest may be indicative of the risk of disease development or the presence or further progression of such disease or disorder.
  • a reference sample may be derived from an abnormal or diseased tissue, organ or individual thereby providing a standard of a diseased status of a tissue, organ or individual.
  • Differences between the status of the abnormal reference sample and the status of the sample of interest may be indicative of a lowered risk of disease development or the absence or bettering of such disease or disorder.
  • a reference sample may also be derived from the same tissue, organ, or individual as the sample of interest but has been taken at an earlier time point. Differences between the status of the earlier taken reference sample and the status of the sample of interest may be indicative of the progression of the disease, i.e. a bettering or worsening of the disease over time.
  • a reference sample was taken at an earlier or later time point in case a period of time has lapsed between taking of the reference sample and taking of the sample of interest. Such period of time may represent years (e.g.
  • a reference sample may be "treated differently” or “exposed differently” than a sample of interest in case both samples are treated in a substantially identical way except from a single factor.
  • single factors include but are not limited to the time of exposure, the concentration of exposure, or the temperature of exposure to a certain substance.
  • a sample of interest may be exposed to a different dosage of a certain substance than the reference sample or may be exposed for a different time interval than the reference sample or may be exposed at a different temperature than the reference sample.
  • Different dosages to which a sample of interest may be exposed to include but are not limited to the 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold and/or 1000-fold increased or decreased dosage of the dosage the reference sample is exposed to.
  • Different exposure times to which a sample of interest may be exposed to include but are not limited to the 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold and/or 1000-fold longer or shorter time period than the exposure of the reference.
  • Different temperatures of exposure to which a sample of interest may be exposed to include but are not limited to the 2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold and/or 1000-fold increased or decreased temperature than the exposure of the reference.
  • a sample of interest may be exposed to a 10-fold increased concentration of a substance than the reference sample.
  • the analysis of both samples is then conducted in a substantially identical manner allowing determining the effects, i.e. a beneficial or an adverse effect, of the increased concentration of such substance on the sample of interest.
  • this example applies mutatis mutandis to different ranges of concentrations, different exposure times, and/or different temperatures at exposure.
  • lowered or decreased level of an indicator refer to the level of such indicator in the sample being reduced in comparison to the reference or reference sample.
  • elevated or increased level of an indicator refer to the level of such indicator in the sample being higher in comparison to the reference or reference sample.
  • Reference amounts can, in principle, be calculated for a group or cohort of subjects as specified herein based on the average or median values for a given miRNA by applying standard methods of statistics.
  • accuracy of a test such as a method aiming to diagnose an event, or not, is best described by its receiver-operating characteristics (ROC) (see especially Zweig 1993, Clin. Chem. 39:561-577 ).
  • the ROC graph is a plot of all of the sensitivity versus specificity pairs resulting from continuously varying the decision threshold over the entire range of data observed.
  • the clinical performance of a diagnostic method depends on its accuracy, i.e. its ability to correctly allocate subjects to a certain prognosis or diagnosis.
  • the ROC plot indicates the overlap between the two distributions by plotting the sensitivity versus 1-specificity for the complete range of thresholds suitable for making a distinction.
  • sensitivity or the true-positive fraction, which is defined as the ratio of number of true-positive test results to the sum of number of true-positive and number of false-negative test results. This has also been referred to as positivity in the presence of a disease or condition. It is calculated solely from the affected subgroup.
  • the false-positive fraction, or 1-specificity which is defined as the ratio of number of false-positive results to the sum of number of true-negative and number of false-positive results. It is an index of specificity and is calculated entirely from the unaffected subgroup.
  • the ROC plot is independent of the prevalence of the event in the cohort.
  • Each point on the ROC plot represents a sensitivity/-specificity pair corresponding to a particular decision threshold.
  • a test with perfect discrimination has an ROC plot that passes through the upper left corner, where the true-positive fraction is 1.0, or 100% (perfect sensitivity), and the false-positive fraction is 0 (perfect specificity).
  • the theoretical plot for a test with no discrimination is a 45° diagonal line from the lower left corner to the upper right corner. Most plots fall in between these two extremes.
  • a threshold can be derived from the ROC curve allowing for the diagnosis or prediction for a given event with a proper balance of sensitivity and specificity, respectively. Accordingly, the reference to be used for the methods of the present invention can be generated, preferably, by establishing a ROC for said cohort as described above and deriving a threshold amount there from.
  • the ROC plot allows deriving suitable thresholds.
  • the reference amounts lie within the range of values that represent a sensitivity of at least 75% and a specificity of at least 45%, or a sensitivity of at least 80% and a specificity of at least 40%, or a sensitivity of at least 85% and a specificity of at least 33%, or a sensitivity of at least 90% and a specificity of at least 25%.
  • the reference amount as used herein is derived from samples of subjects obtained before treatment, but for which it is known if their donors were being afflicted with BC or MBC or not.
  • This reference amount level may be a discrete figure or may be a range of figures.
  • the reference level or amount may vary between individual species of miRNA.
  • the measuring system therefore, preferably, is calibrated with a sample or with a series of samples comprising known amounts of each specific miRNA. It is understood by the skilled person that in such case the amount of miRNA can preferably be expressed as arbitrary units (AU).
  • the amounts of miRNA are determined by comparing the signal obtained from the sample to signals comprised in a calibration curve.
  • the reference amount applicable for an individual subject may vary depending on various physiological parameters such as age or subpopulation.
  • a suitable reference amount may be determined by the methods of the present invention from a reference sample to be analyzed together, i.e. simultaneously or subsequently, with the test sample.
  • a threshold amount can be preferably used as a reference amount.
  • a reference amount may, preferably, be derived from a sample of a subject or group of subjects being afflicted with BC or MBC which is/are known to be afflicted with BC or MBC.
  • a reference amount may, preferably, also be derived from a sample of a subject or group of subjects known to be not afflicted with BC or MBC.
  • a deviation i.e. a decrease or an increase of the miRNA amounts referred to herein is, preferably, a statistically significant deviation, i.e. a statistically significant decrease or a statistically significant increase.
  • treat means accomplishing one or more of the following: (a) reducing the severity of the disorder; (b) limiting or preventing development of symptoms characteristic of the disorder(s) being treated; (c) inhibiting worsening of symptoms characteristic of the disorder(s) being treated; (d) limiting or preventing recurrence of the disorder(s) in an individual that have previously had the disorder(s); and (e) limiting or preventing recurrence of symptoms in individuals that were previously symptomatic for the disorder(s).
  • prevent means preventing that such disease or disorder occurs in patient.
  • the term "therapy” refers to all measures applied to a subject to ameliorate the diseases or disorders referred to herein or the symptoms accompanied therewith to a significant extent. Said therapy as used herein also includes measures leading to an entire restoration of the health with respect to the diseases or disorders referred to herein. It is to be understood that therapy as used in accordance with the present invention may not be effective in all subjects to be treated. However, the term shall require that a statistically significant portion of subjects being afflicted with a disease or disorder referred to herein can be successfully treated. Whether a portion is statistically significant can be determined without further ado by the person skilled in the art using various well known statistic evaluation tools discussed herein above.
  • breast cancer therapy relates to applying to a subject afflicted with breast cancer, including metastasizing breast cancer, measures to remove cancer cells from the subject, to inhibit growth of cancer cells, to kill cancer cells, or to cause the body of a patient to inhibit the growth of or to kill cancer cells.
  • breast cancer therapy is chemotherapy, anti-hormone therapy, targeted therapy, immunotherapy, or any combination thereof. It is, however, also envisaged that the cancer therapy is radiation therapy or surgery, alone or combination with other therapy regimens. It is understood by the skilled person that the selection of the breast cancer therapy depends on several factors, like age of the subject, tumor staging, and receptor status of tumor cells.
  • the selection of the breast cancer therapy can be assisted by the methods of the present invention: if, e.g. BC is diagnosed by the method for diagnosing BC, but no MBC is diagnosed by the method for diagnosing MBC, surgical removal of tumor may be sufficient. If, e.g. BC is diagnosed by the method for diagnosing BC and MBC is diagnosed by the method for diagnosing MBC, therapy measures in addition to surgery, e.g. chemotherapy and / or targeted therapy, may be appropriate. Likewise, if, e.g. BC is diagnosed by the method for diagnosing BC, and an unfavorable CTC status is determined by the method for determining the CTC status, e.g. a further addition of immunotherapy to the therapy regimen may be required.
  • chemotherapy relates to treatment of a subject with an antineoplastic drug.
  • chemotherapy is a treatment including alkylating agents (e.g. cyclophosphamide), platinum (e.g. carboplatin), anthracyclines (e.g. doxorubicin, epirubicin, idarubicin, or daunorubicin) and topoisomerase II inhibitors (e.g. etoposide, irinotecan, topotecan, camptothecin, or VP16), anaplastic lymphoma kinase (ALK)-inhibitors (e.g.
  • alkylating agents e.g. cyclophosphamide
  • platinum e.g. carboplatin
  • anthracyclines e.g. doxorubicin, epirubicin, idarubicin, or daunorubicin
  • topoisomerase II inhibitors e.g. etoposide,
  • aurora kinase inhibitors e.g. N-[4-[4-(4-Methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl]sulfanylphenyl]cyclopropanecarboxamide (VX-680)
  • antiangiogenic agents e.g. Bevacizumab
  • Iodine 131-1-(3-iodobenzyl)guanidine therapeutic metaiodobenzylguanidine
  • HDAC histone deacetylase
  • chemotherapy preferably, relates to a complete cycle of treatment, i.e. a series of several (e.g. four, six, or eight) doses of antineoplastic drug or drugs applied to a subject separated by several days or weeks without such application.
  • anti-hormone therapy relates to breast cancer therapy by blocking hormone receptors, e.g. estrogen receptor or progesterone receptor, expressed on tumor cells, or by blocking the biosynthesis of estrogen.
  • Blocking of hormone receptors can preferably be achieved by administering compounds, e.g. tamoxifen, binding specifically and thereby blocking the activity of said hormone receptors.
  • Blocking of estrogen biosynthesis is preferably achieved by administration of aromatase inhibitors like, e.g. anastrozole or letrozole. It is known to the skilled artisan that anti-hormone therapy is only advisable in cases where tumor cells are expressing hormone receptors.
  • targeted therapy relates to application to a patient a chemical substance known to block growth of cancer cells by interfering with specific molecules known to be necessary for tumorigenesis or cancer or cancer cell growth.
  • Examples known to the skilled artisan are small molecules like, e.g. PARP-inhibitors (e.g. Iniparib), or monoclonal antibodies like, e.g., Trastuzumab.
  • immunotherapy as used herein relates to the treatment of cancer by modulation of the immune response of a subject. Said modulation may be inducing, enhancing, or suppressing said immune response.
  • cell based immunotherapy relates to a breast cancer therapy comprising application of immune cells, e.g. T-cells, preferably tumor-specific NK cells, to a subject.
  • radiation therapy or “radiotherapy” is known to the skilled artisan.
  • the term relates to the use of ionizing radiation to treat or control cancer.
  • the skilled person also knows the term “surgery”, relating to operative measures for treating breast cancer, e.g. excision of tumor tissue.
  • therapy monitoring relates to obtaining an indication on the effect of a treatment against cancer on the cancer status of a subject afflicted with said cancer.
  • therapy monitoring comprises application of a method of the present invention on two samples from the same subject, wherein a first sample is obtained at a time point before the second sample.
  • the time point of obtaining the first sample is separated from the time point of obtaining the second sample by about one week, about two weeks, about three weeks, about for weeks, about five weeks, about, six weeks, about seven weeks, about two months, about three months, about five months, about six month, or more than about six months.
  • the method of therapy monitoring is used for long-term monitoring of subjects, e.g. monitoring the time of relapse-free survival or the like.
  • the time point of obtaining the first sample is separated from the time point of obtaining the second sample, preferably, by at least six months, at least one year, at least two years, at least three years, at least four years, at least five years, or at least six years.
  • the first sample is preferably obtained before cancer therapy is started, while the second sample is preferably obtained after therapy is started. It is, however, also envisaged by the present invention that both samples are obtained after therapy is started.
  • sample obtained at the first point in time may be used as the first sample relative to the second sample as well as for a third sample.
  • the sample obtained at the second point in time may nonetheless be used as a first sample relative to a third sample, and the like.
  • treatment success preferably relates to an amelioration of the diseases or disorders referred to herein or the symptoms accompanied therewith to a significant extent. More preferably, the term relates to a complete cure of said subject, i.e. to the prevention of progression and/or relapse of metastasizing breast cancer for at least five years. Accordingly, "determining treatment success” relates to assessing the probability according to which a subject was successfully treated. Preferably, the term relates to predicting progression free survival and/or overall survival of the subject, more preferably for a specific period of time. The term “predicting progression free survival” relates to determining the probability of a subject surviving without relapse and/or progression of metastatic breast cancer for a specific period of time. Accordingly, the term “predicting overall survival” relates to determining the probability according to which a subject will survive for a specific period of time. Preferably, said period of time is at least 12 months, more preferably at least 24 months.
  • kit refers to a collection of the aforementioned components, preferably, provided separately or within a single container.
  • the container also preferably, comprises instructions for carrying out the method of the present invention. Examples for such the components of the kit as well as methods for their use have been given in this specification.
  • the kit preferably, contains the aforementioned components in a ready-to-use formulation.
  • the kit may additionally comprise instructions, e.g., a user's manual for adjusting the components, e.g. concentrations of the detection agents, and for interpreting the results of any determination(s) with respect to the diagnoses provided by the methods of the present invention.
  • a user's manual for adjusting the components, e.g. concentrations of the detection agents, and for interpreting the results of any determination(s) with respect to the diagnoses provided by the methods of the present invention.
  • such manual may include information for allocating the amounts of the determined a gene product to the kind of diagnosis.
  • Such user's manual may provide instructions about correctly using the components of the kit for determining the amount(s) of the respective biomarker.
  • a user's manual may be provided in paper or electronic form, e.g., stored on CD or CD ROM.
  • the present invention also relates to the use of said kit in any of the methods according to the present invention.
  • the term "device” as used herein relates to a system of means comprising at least the aforementioned means operatively linked to each other as to allow the diagnosis.
  • Preferred means for determining the methylation status or the amount of gene product and means for carrying out the comparison are disclosed above in connection with the methods of the invention. How to link the means in an operating manner will depend on the type of means included into the device. For example, where means for automatically determining the methylation status or the amount of a gene product are applied, the data obtained by said automatically operating means can be processed by, e.g., a computer program in order to establish a diagnosis.
  • the means are comprised by a single device in such a case.
  • Said device may accordingly include an analyzing unit for determining the methylation status or the amount of a gene product in a sample and an evaluation unit for processing the resulting data for the diagnosis.
  • Preferred means for detection are disclosed in connection with embodiments relating to the methods of the invention above.
  • the means are operatively linked in that the user of the system brings together the result of the determination of the amount and the diagnostic value thereof due to the instructions and interpretations given in a manual.
  • the means may appear as separate devices in such an embodiment and are, preferably, packaged together as a kit. The person skilled in the art will realize how to link the means without further inventive skills.
  • Preferred devices are those which can be applied without the particular knowledge of a specialized clinician, e.g., test stripes or electronic devices which merely require loading with a sample.
  • the results may be given as output of parametric diagnostic raw data, preferably, as absolute or relative amounts. It is to be understood that these data will need interpretation by the clinician.
  • expert system devices wherein the output comprises processed diagnostic raw data the interpretation of which does not require a specialized clinician.
  • Further preferred devices comprise the analyzing units/devices (e.g., biosensors, arrays, solid supports coupled to ligands specifically recognizing the polypeptides, Plasmon surface resonance devices, NMR spectrometers, mass- spectrometers etc.) or evaluation units/devices referred to above in accordance with the methods of the invention.
  • analyzing units/devices e.g., biosensors, arrays, solid supports coupled to ligands specifically recognizing the polypeptides, Plasmon surface resonance devices, NMR spectrometers, mass- spectrometers etc.
  • the present invention relates to a method of diagnosing breast cancer (BC) in a subject, comprising
  • miR-652 may refer to the sequence of the -3p or -5p strand (in particular miR-652-3p )
  • miR-801 refers to the sequence of the -3p or -5p strand
  • miR-376c may refer to the sequence of the -3p or -5p strand (in particular miR-376c-3p)
  • miR-376a may refer to the sequence of the -3p or -5p strand (in particular miR-376a-3p)
  • miR-127 may refer to the sequence of the -3p or -5p strand (in particular miR-127-3p)
  • miR-409 may refer to the sequence of the -3p or -5p strand (in particular miR-409-3p)
  • miR-148b may refer to the sequence of the -3p or -5p strand (in particular miR-148-3p).
  • An alteration in the methylation status and/or expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P and/or DYRK4, may indicate a change in tissue status or disease such as the worsening or bettering of a tissue status or disease, in particular cancer.
  • a decreased methylation status ofHYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of a worsening of a tissue status or disease.
  • An increased methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may be indicative of a bettering of a tissue status or disease.
  • An alteration in the methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may also be indicative of the risk of developing an altered tissue status or a disease, in particular cancer.
  • a decreased methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of the risk of developing a degenerative tissue status or disease, in particular cancer.
  • An altered methylation status ofHYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, in particular decreased methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S 100P, and/or DYRK4, may also be indicative of an individual suffering from an altered tissue status or a disease, in particular cancer.
  • an altered methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may indicate the progression or a stage of a tissue status or a disease, in particular cancer, in a subject.
  • a decreased methylation status of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of a worsening of a tissue status or disease, in particular cancer.
  • an increased expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of a worsening of a tissue status or disease.
  • a decreased expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may be indicative of a bettering of a tissue status or disease.
  • An alteration in the expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may also be indicative of the risk of developing an altered tissue status or a disease, in particular cancer.
  • an increased expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of the risk of developing a degenerative tissue status or disease, in particular cancer.
  • An altered expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, in particular increased expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may also be indicative of an individual suffering from an altered tissue status or a disease, in particular cancer.
  • an altered expression level of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, e.g. an elevated or lowered expression level ofHYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4, may indicate the progression or a stage of a tissue status or a disease, in particular cancer, in a subject.
  • an increased expression level ofHYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 may be indicative of a worsening of a tissue status or disease, in particular cancer.
  • An alteration in the miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level may indicate a change in tissue status or disease such as the worsening or bettering of a tissue status or disease, in particular cancer.
  • an elevated level of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b may be indicative of a worsening of a tissue status or disease.
  • a lowered level of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b may be indicative of a bettering of a tissue status or disease.
  • An alteration in the miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level may also be indicative of the risk of developing an altered tissue status or a disease, in particular cancer. More specifically an elevated level of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b may be indicative of the risk of developing a degenerative tissue status or disease, in particular cancer.
  • An altered miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level in particular an elevated miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level, may also be indicative of an individual suffering from an altered tissue status or a disease, in particular cancer.
  • an altered miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level e.g.
  • an elevated or lowered level of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b may indicate the progression or a stage of a tissue status or a disease, in a subject.
  • an elevated miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and/or miR-148b level may be indicative of a worsening of a tissue status or disease, in particular cancer.
  • the methylation status and/or expression level of the at least one methylation marker and the presence, in particular the amount, of at least one miRNA is indicative of the prognosis and/or diagnosis of said subject.
  • the prognosis and/or diagnosis of cancer includes
  • the methylation status of at least 2, 3, 4, 5, 6, 7 or 8 different methylation markers can be determined.
  • all 7 miRNA marker are determined.
  • this combination is reffered to as miR-7, i.e. miR-7 encompasses all seven miRNA marker miR-652, miR-801, miR-376c, miR-376a, miR-127p, miR-409, and miR-148b.
  • methylation marker and miRNAs may be used for prognosing and/or diagnosing cancer.
  • the methylation status of the methylation markers RPTOR, MGRN1 and RAPSN is determined, and the presence, in particular the amount, of the miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127-3p, miR-409-3p and miR-148b is determined.
  • the methylation status and/or expression level of HYAL2 is also determined.
  • the methylation status of the methylation markerw DYRK4, S100P, FUT7 and SLC22A18 is determined, and the presence, in particular the amount, of the miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127-3p, miR-409-3p and miR-148b is determined.
  • the methylation status of HYAL2 is also determined.
  • the methylation status of the methylation markers MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P and DYRK4 is determined, and the presence of the miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127-3p, miR-409-3p and miR-148b is determined.
  • the methylation status of HYAL2 is also determined.
  • the determination of the methylation status may comprise determining methylation of at least one CpG site within the HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and/or DYRK4 gene.
  • the methylation status of the promoter, intron and/or exon region of said genes is determined.
  • the HYAL2 gene is the human HYAL2 gene located on human chromosome 3 (Genbank Acc No: NC_000003.11 GI: 224589815).
  • the methylation status of at least one of the CpG sites located between position 50334760 and position 50335700 on human chromosome 3 is determined.
  • At least one CpG site is selected from the list consisting of cg27091787 at position 50335694, HYAL_CpG_1 at position 50335584, HYAL_CpG_2 at position 50335646, and HYAL_CpG_3 at position 50335671.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined.
  • CpG sites may depend on the specific genomic sequence and on the specific sequence of the HYAL2 promoter region comprised in the sample to be analyzed.
  • the HYAL2 gene is located on Chromosome 3: positions 50,355,221-50,360,337 in build37/hgl9, but on Chromosome 3: positions 50,330,244-50,335,146 in build36/hg18.
  • the MGRN1 gene is the human MGRN1 gene located at human chromosome 16 (Genbank Acc No: NC_000016.10, range: 4624824-4690974, Reference GRCh38 Primary Assembly; Genbank Acc No: NC_018927.2, range: 4674882-4741756, alternate assembly CHM1_1.1; Genbank Acc No: AC_000148.1, range: 4641815-4707494, alternate assembly HuRef).
  • the methylation status of at least one of the CpG sites located between position 4654000 and position 4681000 on human chromosome 16 is determined.
  • the CpG site(s) is/are located in one or more of the following regions of chromosome 16: 4670069-4670542, 4654000-4655000, 4669000-4674000, and 4678000-4681000. More specifically, in particular referring to build 36.1/hg18 of the human genome, the methylation status of at least one of the CpG sites located at position: 4670487 (MGRN1_CpG_1), 4670481 (MGRN1_CpG_2), 4670466 (MGRN1_CpG_3), 4670459 (MGRN1_CpG_4), 4670442 (MGRN1_CpG_5), 4670440 (MGRN1_CpG_6), 4670435 (MGRN1_CpG_7), 4670433 (MGRN1_CpG_8), 4670422 (MGRN1_CpG_9), 4670414 (MGRN1_CpG_10), 4670411 (MGRN1
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the MGRN1 promoter region comprised in the sample to be analyzed.
  • the RPTOR gene is the human RPTOR gene located at human chromosome 17 (Genbank Acc No: NC_000017.11, range: 80544825-80966373, GRCh38 Primary Assembly; Genbank Acc No: NG_013034.1, range: 5001-426549, RefSeqGene; Genbank Acc No: NC_018928.2, range: 78604958-79026514, Alternate assembly CHM1_1.1; Genbank Acc No: NG_013034.1; Genbank Acc No: AC_000149.1,range: 73954508-74378467, alternate assembly HuRef).
  • the methylation status of at least one of the CpG sites located between position 76.297.000 and position 76.416.000 on human chromosome 17 is determined.
  • the CpG site(s) is/are located in one or more of the following regions of chromosome 17: 76.369.937-76.370.536. 76.297.000-76.310.000, 76.333.000-76.341.000, 76.360.000-76.380.000, and 76.411.000-76.416.000.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the
  • the SLC22A18 gene is the human SLC22A18 gene located at human chromosome 11 (Genbank Acc No: NC_000011.10, range: 2899721-2925246, Reference GRCh38 primary assembly; Genbank Acc No: NG_011512.1, range: 5001-30526, RefSeqGene; Genbank Acc No: NT_187585.1, range: 131932-157362, Reference GRCh38 ALT_REF_LOCI_1; Genbank Acc No: AC_000143.1, range: 2709509-2734907, alternate assembly HuRef; Genbank Acc No: NC_018922.2, range:2919878-2945340, alternate assembly CHM1_1.1).
  • the methylation status of at least one of the CpG sites located between position 2876000 and position 2883000 on human chromosome 11 is determined.
  • the CpG sites are located at 2.877.113-2.877.442.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the SLC22A18 promoter region comprised in the sample to be analyzed.
  • the FUT7 gene is the human FUT7 gene located at human chromosome 9 (Genbank Acc No: NC_000009.12, range: 137030174-137032840, Reference GRCh38 primary assembly; Genbank Acc No: NG_007527.1, range: 5001-7667, RefSeqGene; Genbank Acc No: AC_000141.1, range: 109383478-109386144, Alternate assembly HuRef; Genbank Acc No: NC_018920.2, range: 140073389-140076055, Alternate assembly CHM1_1.1).
  • the methylation status of at least one of the CpG sites located between position 139046000 and position 139048000 on human chromosome 9 is determined.
  • a 2000 bp BC, OvaCa, and/or PaCA-associated differential methylation region located at the promoter region of FUT7.
  • the CpG sites are located at 139.047.218-139.047.610, 139.046.000-139.048.000, and 139.045.065-139.045.817.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the FUT7 promoter region comprised in the sample to be analyzed.
  • the RAPSN gene is the human RAPSN gene located at human chromosome 11 (Genbank Acc No: NC_000011.10, range: 47437757-.47449178, Reference GRCh38 primary assembly; Genbank Acc No: NG_008312.1, range: 5001-16423, RefSeqGene; Genbank Acc No: NC_018922.2, range: 47458570-47469991, alternate assembly CHM1_1.1; Genbank Acc No: AC_000143.1, range: 47159075-47170494, alternate assembly HuRef).
  • the methylation status of at least one of the CpG sites located between position 47427500 and position 47428500 on human chromosome 11 is determined.
  • the CpG sites are located at 47427500 -47428300. More specificly, a 1000 bp cancer-associated, preferably BC, OvaCa, and/or PaCA-associated, differential methylation region located at the promoter region of RAPSN.
  • RASN_CpG_1 the methylation status of at least one of the CpG sites located at position: 47427787 (RAPSN_CpG_1), 47427825 (RAPSN_CpG_2), 47427883 (RAPSN_CpG_3), 47427915 (RAPSN_CpG_4), 47427930 (RAPSN_CpG_5), 47427976 (RAPSN_Cp
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the RAPSN promoter region comprised in the sample to be analyzed.
  • the S100P gene is the human S100P gene located at human chromosome 4 (Genbank Acc No: NC_000004.12, range: 6693839-6697170, Reference GRCh38 primary assembly; Genbank Acc No: AC_000136.1, range: 6627254-6630595, alternate assembly HuRef; Genbank Acc No: NC_018915.2, range: 6693944-6697285, alternate assembly CHM1_1.1).
  • the methylation status of at least one of the CpG sites located between position 6746000 and position 6747000 on human chromosome 4 is determined.
  • a 1000 bp cancer-associated (preferably BC, OvaCa, and/or PaCA-associated) differential methylation region located from the promoter region till the first exon of S100P.
  • the CpG sites are located at 6.746.537-6.746.823.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the S100P promoter region comprised in the sample to be analyzed.
  • the DYRK4 gene is the human DYRK4 gene located at human chromosome 12 (Genbank Acc No: NC_000012.12, range: 4590072-4613888, Reference GRCh38 primary assembly; Genbank Acc No: AC_000144.1, range: 4555932-4579747, Alternate assembly HuRef; Genbank Acc No: NC_018923.2, range: 4698860-4722666, alternate assembly CHM1_1.1).
  • the methylation status of at least one of the CpG sites located between position 4569000 and position 4571000 on human chromosome 12 is determined.
  • a 2000 bp cancer-associated, preferably BC, OvaCa, and/or PaCA associated, differential methylation region located at the promoter region of DYRK4.
  • the CpG sites are located at 4569448 -4569945.
  • the methylation status of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least fifteen CpG sites of the present invention is determined. It is understood by the skilled person that the exact numbering of said CpG sites may depend on the specific genomic sequence and on the specific sequence of the DYRK4 promoter region comprised in the sample to be analyzed.
  • the method of prognosing and/or diagnosing cancer may further comprise the step of comparing the methylation status of the at least one methylation marker and the presence, in particular the amount, of the miRNA markers in said subject, to the methylation status of the at least one methylation marker and the presence, in particular the amount, of the miRNA markers in one or more reference(s).
  • the reference is a threshold value, a reference value or a reference sample.
  • a methylation status of the at least on methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4, which is below a threshold value is indicative of a subject being afflicted with cancer, an increased risk of developing cancer, or a worsening of the disease; whereas a methylation status which is equal to or above the threshold value is indicative of a subject not afflicted with cancer, of a decreased risk of developing cancer, or of a bettering of the disease.
  • the aforementioned level may vary due to statistics and errors of measurement.
  • an expression level of the at least on methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4, which is equal to or above the threshold value is indicative of a subject being afflicted with cancer, an increased risk of developing cancer, or a worsening of the disease; whereas an expression level which is below the threshold value is indicative of a subject not being afflicted with cancer, of a decreased risk of developing cancer, or of a bettering of the disease. It is to be understood that the aforementioned level may vary due to statistics and errors of measurement.
  • an amount of the miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409 and miR-148b, which is equal to or above the threshold value is indicative of a subject being afflicted with cancer, an increased risk of developing cancer, or a worsening of the disease; whereas an amount which is below the threshold value is indicative of a subject not being afflicted with cancer, of a decreased risk of developing cancer, or of a bettering of the disease. It is to be understood that the aforementioned amounts may vary due to statistics and errors of measurement.
  • the threshold value for a subject being afflicted with cancer, an increased risk of developing cancer, or a worsening of the disease for HYAL2 can be a methylation status of less than 90% of the controls and an expression level of more than 1.2 folds higher than the controls.
  • the threshold value for MGRN1 can be a methylation status of less than 90% of the controls.
  • the threshold value for RPTOR can be a methylation status of less than 95% of the controls.
  • the threshold value for SLC22A18 can be a methylation status of less than 95% of the controls and an expression level of more than 1.1 folds higher than the controls.
  • the threshold value for FUT7 can be a methylation status of less than 92% of the controls.
  • the threshold value for RAPSN can be a methylation status of less than 98% of the controls.
  • the threshold value for S100P can be a methylation status of less than 90% of the controls and an expression level of more than 2 folds higher than the controls.
  • the threshold value for DYRK4 can be a methylation status of less than 85% of the controls.
  • the threshold level for miR-652 can be an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls).
  • the threshold level for miR-801 can be an amount of at least 0.6Ct value less than the controls (or more than 1.5 folds higher than the controls).
  • the threshold level for miR-376c can be an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls).
  • the threshold level for miR-376a can be an amount of at least 0.6Ct value less than the controls (or more than 1.5 folds higher than the controls).
  • the threshold level for miR-127 can be an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls).
  • the threshold level for miR-409 can be an amount of at least 0.4Ct value less than the controls (or more than 1.3 folds higher than the controls).
  • the threshold level for miR-148b can be an amount of at least 0.3Ct value less than the controls (or more than 1.2 folds higher than the controls).
  • said reference value can be a representative value of the absence of cancer, of the presence of cancer, or of an increased or decreased risk of developing cancer.
  • the reference sample can be selected from the group consisting of a reference sample derived from a healthy individual, a reference sample derived from a diseased individual, a reference sample derived from the same individual as the sample of interest taken at an earlier or later time point, and a reference sample representative for a healthy individual or representative for the presence or absence of cancer or representative for an increased or decreased risk of developing cancer.
  • a decreased methylation level and/or an increased expression of the at least one methylation marker and the presence or an increased amount of the at least one miRNA marker compared to the reference indicates
  • a similar methylation status or expression level of the at least one methylation marker and a similar amount of the at least one miRNA marker indicates
  • the amount of miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409 and miR-148b is determined.
  • an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls) miR-652 is indicative of cancer
  • an amount of at least 0.6Ct value less than the controls (or more than 1.5 folds higher than the controls) miR-801 is indicative of cancer
  • an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls) miR-376c is indicative of cancer
  • an amount of at least 0.6Ct value less than the controls (or more than 1.5 folds higher than the controls) miR-376a is indicative of cancer
  • an amount of at least 0.5Ct value less than the controls (or more than 1.4 folds higher than the controls) miR-127 is indicative of cancer
  • the sample of interest and/or the reference sample can be a body fluid sample or a tissue sample.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid is blood.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject can be a mammal, reptile, or bird.
  • the subject can be selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • the dosage of a pharmaceutical is determined depending on the comparison of the methylation status and/or expression level of at least one methylation marker and the amount of at least one miRNA marker a in the sample of interest and the reference or reference sample.
  • the sample of interest and/or the reference sample is a body fluid samples or a tissue samples.
  • the body fluid sample is selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid is blood.
  • the tissue sample is preferably a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject can be a mammal, reptile, or bird.
  • the subject is selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • the dosage of a pharmaceutical is increased if
  • the dosage of a pharmaceutical is decreased if
  • the sample of interest and/or the reference sample can be a body fluid sample or a tissue sample.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid sample can be a blood sample.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject is a mammal, reptile, or bird.
  • the subject is selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • the sample of interest can be exposed differently to said substance with regard to time and/or concentration.
  • the sample of interest may be exposed to said substance for a longer or shorter time interval, and/or at a higher or lower concentration of said substance.
  • a beneficial effect of a substance is determined if
  • a beneficial effect of a substance is determined if
  • the sample of interest and/or the reference sample is a body fluid samples or a tissue samples.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid sample can be a blood sample.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject is a mammal, reptile, or bird.
  • the subject is selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • Also disclosed but nor forming part of the present invention is a method for identifying a patient as a responder to a cancer treatment, comprising determining the methylation status and/or expression level of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4, as specified in detail above, and the amount of at least one miRNA marker selected from the group consisting of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, miR-148b, as specified in detail above, in a first sample and in one or more further samples taken from the subject subsequently to the first sample, wherein an increased methylation status of the at least one methylation marker and/or a lower expression level of the at least one methylation marker, and the absence or decreased amount of the at least one miRNA marker indicates a response to the treatment.
  • the sample of interest and/or the reference sample may be a body fluid sample or a tissue sample.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid sample is a blood sample.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject can be a mammal, reptile, or bird.
  • the subject is selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • Also disclosed but not forming part of the present invention is a method for identifying a patient as a non-responder to a cancer treatment, comprising determining the methylation status and/or expression level of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4, as specified in detail above, and the amount of at least one miRNA marker selected from the group consisting of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, miR-148b, as specified in detail above, in a first sample and in one or more further samples taken subsequently to the first sample, wherein a decreased methylation status of the at least one methylation marker and/or an increased expression level of the at least one methylation marker, and the presence or increased amount of the at least one miRNA marker indicates a lack of response to the treatment.
  • the sample of interest and/or the reference sample can be a body fluid sample or a tissue sample.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells.
  • the sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject can be a mammal, reptile, or bird.
  • the subject can be selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • Also disclosed but not forming part of the present invention is a method for treating cancer, comprising the steps:
  • the sample of interest and/or the reference sample can be a body fluid sample or a tissue sample.
  • the body fluid sample can be selected from the group consisting of blood, serum, plasma, synovial fluid, urine, saliva, lymphatic fluid, lacrimal fluid, and fluid obtainable from the glands such as e.g. breast or prostate.
  • the body fluid sample is a blood sample.
  • the tissue sample can be a tissue extract obtained from tumour tissue or tissue adjacent to a tumour.
  • the sample of interest and/or the reference sample can be a cell culture or tissue culture such as but not limited to cultures of various cancer cells. IThe sample of interest and/or the reference sample can be a medium obtained from said cell cultures or tissue cultures.
  • the subject can be a mammal, reptile, or bird.
  • the subject can be selected from the group consisting of laboratory animals (e.g. mouse or rat), domestic animals (including e.g. guinea pig, rabbit, horse, donkey, cow, sheep, goat, pig, chicken, camel, cat, dog, turtle, tortoise, snake, or lizard), or primates including chimpanzees, bonobos, gorillas, and human being. Human beings are particularly preferred.
  • the treatment regime can be selected from the list consisting of chemotherapy, anti-hormone therapy, immunotherapy, and radiation therapy.
  • Said means may detect the methylation status and/or expression level of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, DYRK4, as specified in detail above.
  • the one or more means for detecting the methylation status of at least one methylation marker may comprise at least one methylation-specific polynucleotide.
  • the methylation-specific polynucleotide can be a methylation-specific primer and/or a methylation-specific probe.
  • the one or more means for detecting the expression level of at least one methylation marker may comprise a binding moiety.
  • Said binding moiety is in particular a polynucleotide, peptide, protein, or aptamer.
  • the binding moiety may be selected from the group consisting of monoclonal antibodies, polyclonal antibodies, Fab fragments, Fc fragments, Fab' fragments, F(ab')2 fragments, single domain antibodies (sdAb), nanobodies, single chain Fv (scFv), divalent single-chain variable fragments (di-scFvs), tandem scFvs, diabodies, triabodies, bispecific diabodies, single-chain diabodies (scDb), bispecific T-cell engagers (BiTEs), and DART" molecules.
  • the binding moiety may bind to a part of the gene product of the methylation marker. Accordingly, in cases wherein the binding moiety is a polynucleotide, said polynucleotide binds to the mRNA transcribed from the gene of the respective methylation marker, i.e. the gene of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, or DYRK4.
  • binding moiety is a peptide, protein or aptamer
  • said peptide, protein, or aptamer binds to a part, in particular an epitope, of the protein translated from the gene of the respective methylation marker, i.e. the gene of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, or DYRK4.
  • Said means may detect at least one miRNA marker selected from the group consisting of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, miR-148b, as specified in detail above.
  • the one or more means for detecting the amount of at least one miRNA marker may comprise at least one miRNA specific polynucleotide.
  • said at least one miRNA specific polynucleotide may have a sequence according to SEQ ID NO: 1-13
  • the said means may be for use in the method of specified in detail above.
  • said means are for use in a method selected from the group consisting of:
  • the present invention relates to the use of a kit for diagnosing BC, the kit comprising one or more means for detecting the methylation status of at least one methylation marker selected from the group consisting of HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P and DYRK4, as specified in detail above, and means for detecting the amount of miRNA markers miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409 and miR-148b, as specified in detail above.
  • the kit may further comprise
  • kit disclosed herein can be used in the method specified in detail above.
  • the kit can be for use in a method selected from the group consisting of:
  • Said means and/or said kit can be used in one of the methods specified in detail above. In particular, they can be used in a method selected from the group consisting of:
  • the present invention relates to the device for identifying BC, comprising:
  • Particular devices are those which can be applied without the particular knowledge of a specialized clinician, e.g., test stripes or electronic devices which merely require loading with a sample.
  • the results may be given as output of parametric diagnostic raw data, in particular, as absolute or relative amounts. It is to be understood that these data will need interpretation by the clinician.
  • expert system devices wherein the output comprises processed diagnostic raw data the interpretation of which does not require a specialized clinician.
  • Further preferred devices comprise the analyzing units/devices (e.g., biosensors, arrays, solid supports coupled to ligands specifically recognizing the miRNAs of the present invention, Plasmon surface resonance devices, NMR spectrometers, mass- spectrometers etc.) or evaluation units/devices.
  • Genomic DNA was isolated from peripheral whole blood using DNA isolation kits from Qiagen.
  • the leucocytes were immediately frozen in liquid nitrogen after isolation and stored at -80°C until use.
  • DNA and RNA were isolated from leucocytes using AllPrep DNA/RNA/Protein Mini Kit from Qiagen. Detailed information for the samples was shown in Table 1. Please see the clinical data of the sporadic BC patients in Table 5 and Table 6.
  • Peripheral blood samples from 270 BRCA1/2 mutation-negative index familial BC patients were collected by the centers of the German Consortium for Hereditary Breast and Ovarian Cancer in Heidelberg and Cologne. All the familial BC cases were recruited according to the criteria of family history.
  • Peripheral blood samples from 350 sporadic BC patients (189 in the second validation round and 161 in the third validation round) were collected at the time point of first BC diagnosis before any BC treatment and surgery at the University Hospital of Heidelberg. The clinical characteristics of sporadic BC patients were defined according to the American Joint Committee on Cancer (AJCC) cancer staging manual.
  • AJCC American Joint Committee on Cancer
  • Peripheral blood samples from 459 healthy female controls (251 in the first validation round and 189 in the second validation round) were collected from blood donors by the German Red Cross Blood Service of Baden-written-Hessen.
  • Peripheral blood samples from 151 healthy female controls (third validation round) were collected at the University Hospital of Heidelberg. All the cases and controls in the third validation round were processed with the same manner in parallel.
  • Leucocytes were isolated from peripheral blood using red blood cell lysis buffer within four hours after blood collection at the University Hospital of Heidelberg. All the leucocytes from cases and controls were processed in parallel.
  • Peripheral blood samples from 147 sporadic PaCa patients were collected from multiple centers in Germany. The PaCa cases were specially selected with higher percentage of early stage cases.
  • Peripheral blood samples from 191 healthy controls were collected from blood donors by the German Red Cross Blood Service of Baden - beforehand-Hessen.
  • Peripheral blood samples from 84 sporadic OvCa patients were collected at the University Hospital of Heidelberg.
  • the OvCa cases were specially selected with higher percentage of early stage cases.
  • Peripheral blood samples from 148 healthy controls were collected at the University Hospital of Heidelberg.
  • MALDI-TOF mass spectrometry described by Breitling et al. ( Breitling LP, Yang R, Korn B, Burwinkel B, Brenner H. Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am J Hum Genet 2011;88:450-7 .) was used in various verification rounds. DNA was bisulfite converted by EZ-96 DNA Methylation Gold Kit (Zymo Research) and amplified by bisulfite-specific primers ( Fig. 1 ). The PCR products were treated according to the standard protocol of Sequenom EpiTyper Assay and dispensed to a 384 SpectroCHIP by a Nanodispenser. The chips were read by a Sequenom Mass Spectrometer system. Data were collected by SpectroACQUIRE v3.3.1.3 software and visualized with MassArray EpiTyper v1.0 software. 5% samples were randomly chosen for the duplication analysis.
  • RNA from each sample was transcribed to cDNA by TaqMan® Reverse Transcription Reagents (Applied Biosystems).
  • Quantitative real-time PCR was performed using a LightCycler480 (Roche) in combination with TaqMan gene expression assays (Applied Biosystems) for HYAL2, MGRN1, RPTOR, SLC22A18, FUT7, RAPSN, S100P, and DYRK4 gene and housekeeping gene HPRT1 as endogenous control.
  • Crossing point values were calculated using the second-derivative maximum method by the LightCycler 480 basic software (Roche). Relative expression of genes for each sample was calculated according to the ⁇ Ct method by normalization to HPRT1.
  • the Illumina 27K Array data were processed by the Illumina BeadStudio software with default settings. Probes with detection P-value > 0.01 were removed and samples were quantile-normalized. Association of probes with case/control status was assessed by beta-regression models with a logistic link and associated Wald tests using the R package betareg v2.2-3 30. Likelihood ratio tests were used to compare the case/control model with the nested model for chip differences in order to identify possible false hits due to confounding by chip effects. Multiple testing adjustments were done with the Benjamini-Hochberg method controlling the false discovery rate at the level of 0.05. All analysis was performed with the statistical software R v2.11.1. All the statistical analyses of the gene expression data were conducted by SPSS Statistics 17.0 software.
  • ROC Receiver operating characteristic
  • EDTA blood samples were collected from cases and control individuals and processed for plasma within 2 hours of collection. To avoid contamination with epithelial cells from the initial skin puncture the first blood tube collected during phlebotomy was not processed for plasma. Blood was centrifuged at 1300g for 20 minutes at 10°C. The supernatant (plasma) was transferred into microcentrifuge tubes followed by a second high-speed centrifugation step at 15500 g for 10 minutes at 10°C to remove cell debris and fragments. The plasma was aliquoted into cryo vials, snap-frozen in liquid nitrogen and stored at -80°C until use. Total RNA (including miRNAs) was extracted from 400 ⁇ L of plasma.
  • RT Reverse transcription
  • Singleplex (primary breast cancer) or multiplex (metastatic breast cancer) reactions were carried out in a volume of 7.5 ⁇ l or 15 ⁇ l, respectively.
  • Each reaction comprised 1x RT buffer, 1 mM dNTPs, 0.3x miRNA-specific RT primers, 0.25 U RNase inhibitor, 3.3U Multiscribe Reverse Transcriptase and a fixed volume of miRNA template (2 or 1 ⁇ l, respectively).
  • the reactions were carried out in 15 ⁇ l and comprised the following: 1 x RT buffer, 1mM dNTPs, 0.6x miRNA-specific and RNU6B RT primers, 0.25U RNase inhibitor, 3.3U Multiscribe Reverse Transcriptase and 5 ng RNA. Blinding of samples and a randomized, simultaneous investigation of cases and controls on reaction plates was intended to minimize bias and batch effects during validation.
  • RT was carried out in a G-STORM GS2 PCR cycler (Alphametrix, Germany) under the following conditions: 16°C for 30 min, 42°C for 30 min and 85°C for 5 min, followed by a hold at 4°C.
  • TaqMan real-time PCR reactions were performed in triplicates in scaled-down reactions comprising 2.5 ⁇ L TaqMan 2x Universal PCR Master Mix with No AmpErase UNG (Applied Biosystems, Germany), 0.25 ⁇ L 20x miRNA-specific primer/probe mix (Applied Biosystems, Germany) and 2.25 ⁇ L of the reverse transcription product (diluted 1:4).
  • Real-time PCR was carried out in a LightCycler 480 thermocycler (Roche, Germany) under the following conditions: 95°C for 10 min, then 50 cycles of 95°C for 15 s, 60°C for 30 s and 72°C for 30 s, followed by a hold at 4°C.
  • Raw data from validation studies in blood plasma was normalized to spiked-in cel-miR-39 as described in Kroh et al. ( Kroh EM, Parkin RK, Mitchell PS, Tewari M. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 2010;50:298-301 ).
  • Raw Ct values from breast tissue samples were normalized to RNU6B as described in User Bulletin #2: ABI PRISM 7700 Sequence Detection System (Applied Biosystems).
  • ROC receiver operating characteristic
  • ROC curve analysis was performed to evaluate the diagnostic potential of miR-652, miR-801, miR-376c, miR-376a, miR-127, miR-409, and miR-148b for breast cancer and prostate cancer detection in blood plasma.
  • the discriminatory power between tumor and control samples is depicted by the areas under the curves (AUC).
  • AUC areas under the curves
  • Peripheral blood samples from 161 sporadic BC patients were collected at the time point of first BC diagnosis before any BC treatment and surgery at the University Hospital of Heidelberg.
  • the clinical characteristics of sporadic BC patients were defined according to the American Joint Committee on Cancer (AJCC) cancer staging manual.
  • Peripheral blood samples from 151 healthy female controls were collected at the University Hospital of Heidelberg. All the cases and controls in the third validation round were processed with the same manner in parallel. The DNA from the whole blood and the miRNA from plasma were extracted from each sample.
  • DNA methylation level Determination of DNA methylation level and miRNA level.
  • the DNA methylation levels were determined by MALDI-TOF mass spectrometry (Sequenom) as described in Example 1.
  • the miRNA levels from Alfam were determined by real-time PCR as described in Exapmle 2.

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